Starting phenix.real_space_refine on Fri Dec 27 20:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j4x_61138/12_2024/9j4x_61138.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j4x_61138/12_2024/9j4x_61138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j4x_61138/12_2024/9j4x_61138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j4x_61138/12_2024/9j4x_61138.map" model { file = "/net/cci-nas-00/data/ceres_data/9j4x_61138/12_2024/9j4x_61138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j4x_61138/12_2024/9j4x_61138.cif" } resolution = 2.9 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= -0.002 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 30 5.16 5 C 4462 2.51 5 N 1024 2.21 5 O 1068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.63, per 1000 atoms: 0.70 Number of scatterers: 6588 At special positions: 0 Unit cell: (125.19, 66.34, 75.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 4 15.00 O 1068 8.00 N 1024 7.00 C 4462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.66 Conformation dependent library (CDL) restraints added in 906.7 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 267 through 296 removed outlier: 3.686A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 337 through 340 removed outlier: 3.530A pdb=" N SER A 340 " --> pdb=" O ALA A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.979A 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 403 removed outlier: 3.571A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.723A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.575A pdb=" N CYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 472 through 503 removed outlier: 3.934A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 4.334A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 582 removed outlier: 4.081A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 618 Proline residue: A 598 - end of helix removed outlier: 3.750A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.605A pdb=" N GLU A 622 " --> pdb=" O ASN A 619 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A 623 " --> pdb=" O CYS A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 623' Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.782A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 345 through 360 removed outlier: 4.081A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 417 removed outlier: 5.940A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 472 through 499 removed outlier: 4.285A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.588A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 581 removed outlier: 3.522A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 619 Proline residue: B 598 - end of helix removed outlier: 3.760A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 removed outlier: 4.414A pdb=" N PHE B 623 " --> pdb=" O CYS B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 620 through 623' 438 hydrogen bonds defined for protein. 1311 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: 1.78 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 989 1.32 - 1.44: 2066 1.44 - 1.57: 3691 1.57 - 1.69: 8 1.69 - 1.81: 42 Bond restraints: 6796 Sorted by residual: bond pdb=" CG GLN A 399 " pdb=" CD GLN A 399 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.11e-01 bond pdb=" C ALA A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.26e-01 bond pdb=" N GLY A 589 " pdb=" CA GLY A 589 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.89e-01 bond pdb=" C VAL B 567 " pdb=" O VAL B 567 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.38e-01 bond pdb=" CB CYS B 463 " pdb=" SG CYS B 463 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.56e-01 ... (remaining 6791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 8820 1.11 - 2.21: 315 2.21 - 3.32: 39 3.32 - 4.43: 14 4.43 - 5.53: 14 Bond angle restraints: 9202 Sorted by residual: angle pdb=" N GLU A 260 " pdb=" CA GLU A 260 " pdb=" C GLU A 260 " ideal model delta sigma weight residual 114.62 109.21 5.41 1.14e+00 7.69e-01 2.26e+01 angle pdb=" CA GLU A 260 " pdb=" C GLU A 260 " pdb=" N THR A 261 " ideal model delta sigma weight residual 119.71 115.09 4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" N ARG A 270 " pdb=" CA ARG A 270 " pdb=" C ARG A 270 " ideal model delta sigma weight residual 114.75 110.75 4.00 1.26e+00 6.30e-01 1.01e+01 angle pdb=" C ILE A 269 " pdb=" N ARG A 270 " pdb=" CA ARG A 270 " ideal model delta sigma weight residual 121.52 126.81 -5.29 1.74e+00 3.30e-01 9.23e+00 angle pdb=" N VAL A 509 " pdb=" CA VAL A 509 " pdb=" C VAL A 509 " ideal model delta sigma weight residual 113.00 109.06 3.94 1.30e+00 5.92e-01 9.17e+00 ... (remaining 9197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 3592 16.54 - 33.08: 236 33.08 - 49.61: 62 49.61 - 66.15: 25 66.15 - 82.69: 3 Dihedral angle restraints: 3918 sinusoidal: 1668 harmonic: 2250 Sorted by residual: dihedral pdb=" CA ILE A 269 " pdb=" C ILE A 269 " pdb=" N ARG A 270 " pdb=" CA ARG A 270 " ideal model delta harmonic sigma weight residual 180.00 148.18 31.82 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA PHE A 257 " pdb=" C PHE A 257 " pdb=" N LYS A 258 " pdb=" CA LYS A 258 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA THR A 383 " pdb=" C THR A 383 " pdb=" N ALA A 384 " pdb=" CA ALA A 384 " ideal model delta harmonic sigma weight residual 180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 659 0.035 - 0.069: 239 0.069 - 0.103: 73 0.103 - 0.138: 13 0.138 - 0.172: 2 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB ILE A 269 " pdb=" CA ILE A 269 " pdb=" CG1 ILE A 269 " pdb=" CG2 ILE A 269 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA TRP A 266 " pdb=" N TRP A 266 " pdb=" C TRP A 266 " pdb=" CB TRP A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 983 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 563 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE A 563 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 563 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 564 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 566 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ASP A 566 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 566 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 567 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 306 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 307 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.018 5.00e-02 4.00e+02 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 101 2.69 - 3.24: 6660 3.24 - 3.80: 11036 3.80 - 4.35: 14289 4.35 - 4.90: 24201 Nonbonded interactions: 56287 Sorted by model distance: nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.140 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU B 318 " pdb=" OH TYR B 367 " model vdw 2.225 3.040 nonbonded pdb=" NH2 ARG A 466 " pdb=" O GLY A 621 " model vdw 2.241 3.120 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.247 3.040 ... (remaining 56282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.840 Find NCS groups from input model: 0.180 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 0.028 6796 Z= 0.205 Angle : 0.517 5.533 9202 Z= 0.294 Chirality : 0.039 0.172 986 Planarity : 0.004 0.033 1098 Dihedral : 12.984 82.689 2466 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.33 % Allowed : 6.05 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.84 (0.30), residues: 756 helix: 1.42 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -2.42 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.004 0.001 HIS B 313 PHE 0.015 0.001 PHE B 610 TYR 0.012 0.001 TYR A 553 ARG 0.002 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.740 Fit side-chains REVERT: A 318 GLU cc_start: 0.8815 (tt0) cc_final: 0.8511 (tt0) REVERT: A 376 LYS cc_start: 0.7836 (mttt) cc_final: 0.7308 (mmtm) REVERT: A 394 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 471 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7800 (mmtm) REVERT: A 506 ASP cc_start: 0.7111 (m-30) cc_final: 0.6883 (p0) REVERT: A 523 CYS cc_start: 0.8530 (t) cc_final: 0.8153 (m) REVERT: A 538 ASP cc_start: 0.8084 (t70) cc_final: 0.7499 (t0) REVERT: B 265 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7777 (pp) REVERT: B 472 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7326 (mtm110) REVERT: B 497 SER cc_start: 0.8204 (m) cc_final: 0.7959 (p) REVERT: B 508 MET cc_start: 0.7624 (mmm) cc_final: 0.6439 (mtp) REVERT: B 538 ASP cc_start: 0.7456 (t0) cc_final: 0.6865 (t0) REVERT: B 549 GLU cc_start: 0.8354 (tt0) cc_final: 0.8140 (tt0) REVERT: B 550 GLU cc_start: 0.7290 (pt0) cc_final: 0.6684 (pm20) REVERT: B 608 ASN cc_start: 0.8743 (m-40) cc_final: 0.8476 (m110) outliers start: 9 outliers final: 1 residues processed: 126 average time/residue: 1.0227 time to fit residues: 136.5791 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6796 Z= 0.225 Angle : 0.535 7.758 9202 Z= 0.289 Chirality : 0.041 0.179 986 Planarity : 0.004 0.041 1098 Dihedral : 12.437 64.547 1038 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.21 % Allowed : 10.62 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.40 (0.30), residues: 756 helix: 1.95 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.38 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 395 HIS 0.004 0.001 HIS B 313 PHE 0.022 0.002 PHE B 511 TYR 0.018 0.002 TYR A 352 ARG 0.003 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.760 Fit side-chains REVERT: A 376 LYS cc_start: 0.7836 (mttt) cc_final: 0.7324 (mmtm) REVERT: A 471 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7908 (mmtm) REVERT: A 523 CYS cc_start: 0.8811 (t) cc_final: 0.8497 (m) REVERT: A 538 ASP cc_start: 0.8090 (t70) cc_final: 0.7486 (t0) REVERT: B 265 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7636 (pp) REVERT: B 301 LEU cc_start: 0.9202 (tp) cc_final: 0.8955 (tp) REVERT: B 472 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7273 (mtm110) REVERT: B 497 SER cc_start: 0.8198 (m) cc_final: 0.7915 (p) REVERT: B 508 MET cc_start: 0.7619 (mmm) cc_final: 0.6441 (mtp) REVERT: B 538 ASP cc_start: 0.7453 (t0) cc_final: 0.6858 (t0) REVERT: B 549 GLU cc_start: 0.8368 (tt0) cc_final: 0.8136 (tt0) REVERT: B 550 GLU cc_start: 0.7255 (pt0) cc_final: 0.6596 (pm20) REVERT: B 577 ILE cc_start: 0.7207 (tt) cc_final: 0.6800 (pt) REVERT: B 608 ASN cc_start: 0.8737 (m-40) cc_final: 0.8469 (m110) outliers start: 15 outliers final: 5 residues processed: 118 average time/residue: 0.9646 time to fit residues: 121.4934 Evaluate side-chains 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 0.0060 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 576 GLN B 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6796 Z= 0.190 Angle : 0.506 7.032 9202 Z= 0.273 Chirality : 0.040 0.175 986 Planarity : 0.004 0.035 1098 Dihedral : 12.239 63.102 1036 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.06 % Allowed : 12.68 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 756 helix: 2.07 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.24 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 395 HIS 0.003 0.001 HIS B 313 PHE 0.017 0.001 PHE B 511 TYR 0.024 0.002 TYR A 496 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.641 Fit side-chains REVERT: A 376 LYS cc_start: 0.7817 (mttt) cc_final: 0.7310 (mmtm) REVERT: A 471 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7776 (mmtt) REVERT: A 523 CYS cc_start: 0.8813 (t) cc_final: 0.8497 (m) REVERT: A 538 ASP cc_start: 0.8113 (t70) cc_final: 0.7506 (t0) REVERT: B 265 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7579 (pp) REVERT: B 301 LEU cc_start: 0.9217 (tp) cc_final: 0.8988 (tp) REVERT: B 354 PHE cc_start: 0.8371 (t80) cc_final: 0.8132 (t80) REVERT: B 472 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7316 (mtm110) REVERT: B 497 SER cc_start: 0.8257 (m) cc_final: 0.7777 (p) REVERT: B 508 MET cc_start: 0.7506 (mmm) cc_final: 0.6313 (mtp) REVERT: B 538 ASP cc_start: 0.7465 (t0) cc_final: 0.6900 (t0) REVERT: B 549 GLU cc_start: 0.8362 (tt0) cc_final: 0.8081 (tt0) REVERT: B 550 GLU cc_start: 0.7259 (pt0) cc_final: 0.6693 (pm20) REVERT: B 577 ILE cc_start: 0.7340 (tt) cc_final: 0.6869 (pt) REVERT: B 608 ASN cc_start: 0.8691 (m-40) cc_final: 0.8411 (m110) outliers start: 14 outliers final: 4 residues processed: 115 average time/residue: 1.0373 time to fit residues: 126.6976 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6796 Z= 0.183 Angle : 0.500 6.787 9202 Z= 0.269 Chirality : 0.040 0.173 986 Planarity : 0.004 0.036 1098 Dihedral : 12.083 62.832 1034 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.36 % Allowed : 13.42 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.69 (0.30), residues: 756 helix: 2.17 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 395 HIS 0.003 0.001 HIS B 313 PHE 0.015 0.001 PHE B 610 TYR 0.025 0.002 TYR A 496 ARG 0.004 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.765 Fit side-chains REVERT: A 259 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6500 (tt) REVERT: A 290 TYR cc_start: 0.8787 (t80) cc_final: 0.8586 (t80) REVERT: A 376 LYS cc_start: 0.7809 (mttt) cc_final: 0.7309 (mmtm) REVERT: A 394 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7769 (t80) REVERT: A 470 THR cc_start: 0.8421 (m) cc_final: 0.8015 (p) REVERT: A 471 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7910 (mmtt) REVERT: A 523 CYS cc_start: 0.8838 (t) cc_final: 0.8531 (m) REVERT: A 538 ASP cc_start: 0.8095 (t70) cc_final: 0.7486 (t0) REVERT: B 265 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7616 (pp) REVERT: B 354 PHE cc_start: 0.8293 (t80) cc_final: 0.8025 (t80) REVERT: B 472 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7313 (mtm110) REVERT: B 497 SER cc_start: 0.8237 (m) cc_final: 0.7743 (p) REVERT: B 508 MET cc_start: 0.7474 (mmm) cc_final: 0.6303 (mtp) REVERT: B 538 ASP cc_start: 0.7471 (t0) cc_final: 0.6902 (t0) REVERT: B 549 GLU cc_start: 0.8385 (tt0) cc_final: 0.8083 (tt0) REVERT: B 550 GLU cc_start: 0.7268 (pt0) cc_final: 0.6689 (pm20) REVERT: B 577 ILE cc_start: 0.7386 (tt) cc_final: 0.6916 (pt) REVERT: B 608 ASN cc_start: 0.8662 (m-40) cc_final: 0.8371 (m110) outliers start: 16 outliers final: 7 residues processed: 121 average time/residue: 0.9979 time to fit residues: 128.4066 Evaluate side-chains 109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6796 Z= 0.205 Angle : 0.510 6.662 9202 Z= 0.273 Chirality : 0.040 0.175 986 Planarity : 0.004 0.039 1098 Dihedral : 12.127 62.900 1034 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.51 % Allowed : 14.31 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.68 (0.30), residues: 756 helix: 2.12 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 573 HIS 0.004 0.001 HIS B 313 PHE 0.016 0.001 PHE B 391 TYR 0.026 0.002 TYR A 496 ARG 0.003 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.715 Fit side-chains REVERT: A 259 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6529 (tt) REVERT: A 376 LYS cc_start: 0.7826 (mttt) cc_final: 0.7319 (mmtm) REVERT: A 394 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 470 THR cc_start: 0.8454 (m) cc_final: 0.8091 (p) REVERT: A 471 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7943 (mmtt) REVERT: A 523 CYS cc_start: 0.8857 (t) cc_final: 0.8535 (m) REVERT: A 538 ASP cc_start: 0.8103 (t70) cc_final: 0.7488 (t0) REVERT: B 265 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7625 (pp) REVERT: B 354 PHE cc_start: 0.8260 (t80) cc_final: 0.7936 (t80) REVERT: B 394 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 497 SER cc_start: 0.8228 (m) cc_final: 0.7725 (p) REVERT: B 508 MET cc_start: 0.7520 (mmm) cc_final: 0.6335 (mtp) REVERT: B 538 ASP cc_start: 0.7503 (t0) cc_final: 0.6919 (t0) REVERT: B 549 GLU cc_start: 0.8401 (tt0) cc_final: 0.8096 (tt0) REVERT: B 550 GLU cc_start: 0.7291 (pt0) cc_final: 0.6692 (pm20) REVERT: B 577 ILE cc_start: 0.7368 (tt) cc_final: 0.6856 (pt) REVERT: B 608 ASN cc_start: 0.8675 (m-40) cc_final: 0.8405 (m110) outliers start: 17 outliers final: 7 residues processed: 115 average time/residue: 0.9142 time to fit residues: 112.4670 Evaluate side-chains 109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 73 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6796 Z= 0.171 Angle : 0.491 6.578 9202 Z= 0.265 Chirality : 0.039 0.169 986 Planarity : 0.004 0.038 1098 Dihedral : 12.010 61.687 1034 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.36 % Allowed : 14.75 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.80 (0.30), residues: 756 helix: 2.20 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -2.02 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 395 HIS 0.003 0.001 HIS B 313 PHE 0.015 0.001 PHE B 610 TYR 0.027 0.002 TYR A 496 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8775 (t80) cc_final: 0.8558 (t80) REVERT: A 376 LYS cc_start: 0.7765 (mttt) cc_final: 0.7257 (mmtm) REVERT: A 470 THR cc_start: 0.8440 (m) cc_final: 0.8078 (p) REVERT: A 471 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7936 (mmtt) REVERT: A 523 CYS cc_start: 0.8839 (t) cc_final: 0.8525 (m) REVERT: A 538 ASP cc_start: 0.8101 (t70) cc_final: 0.7418 (t0) REVERT: B 265 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7552 (pp) REVERT: B 354 PHE cc_start: 0.8181 (t80) cc_final: 0.7897 (t80) REVERT: B 394 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 472 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7171 (mtp85) REVERT: B 497 SER cc_start: 0.8200 (m) cc_final: 0.7697 (p) REVERT: B 508 MET cc_start: 0.7428 (mmm) cc_final: 0.6277 (mtp) REVERT: B 538 ASP cc_start: 0.7492 (t0) cc_final: 0.6909 (t0) REVERT: B 577 ILE cc_start: 0.7355 (tt) cc_final: 0.6825 (pt) REVERT: B 608 ASN cc_start: 0.8639 (m-40) cc_final: 0.8347 (m110) outliers start: 16 outliers final: 8 residues processed: 114 average time/residue: 0.9046 time to fit residues: 110.1397 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6796 Z= 0.247 Angle : 0.534 8.735 9202 Z= 0.283 Chirality : 0.041 0.171 986 Planarity : 0.004 0.042 1098 Dihedral : 12.214 63.392 1034 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.65 % Allowed : 14.75 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 756 helix: 1.98 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.14 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 573 HIS 0.005 0.001 HIS B 313 PHE 0.016 0.002 PHE A 605 TYR 0.028 0.002 TYR A 496 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7848 (mttt) cc_final: 0.7323 (mmtm) REVERT: A 470 THR cc_start: 0.8421 (m) cc_final: 0.8068 (p) REVERT: A 471 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7934 (mmtt) REVERT: A 523 CYS cc_start: 0.8894 (t) cc_final: 0.8563 (m) REVERT: A 538 ASP cc_start: 0.8090 (t70) cc_final: 0.7408 (t0) REVERT: B 265 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7582 (pp) REVERT: B 394 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 497 SER cc_start: 0.8202 (m) cc_final: 0.7683 (p) REVERT: B 508 MET cc_start: 0.7462 (mmm) cc_final: 0.6276 (mtp) REVERT: B 538 ASP cc_start: 0.7488 (t0) cc_final: 0.6884 (t0) REVERT: B 577 ILE cc_start: 0.7403 (tt) cc_final: 0.6814 (pt) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 0.9407 time to fit residues: 110.7199 Evaluate side-chains 110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6796 Z= 0.186 Angle : 0.506 8.735 9202 Z= 0.271 Chirality : 0.039 0.171 986 Planarity : 0.004 0.041 1098 Dihedral : 12.054 60.829 1034 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.36 % Allowed : 14.90 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 756 helix: 2.04 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.07 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 573 HIS 0.003 0.001 HIS B 313 PHE 0.016 0.001 PHE B 610 TYR 0.028 0.002 TYR A 496 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7813 (mttt) cc_final: 0.7310 (mmtm) REVERT: A 470 THR cc_start: 0.8327 (m) cc_final: 0.7889 (p) REVERT: A 489 MET cc_start: 0.8734 (ttp) cc_final: 0.8525 (ttp) REVERT: A 523 CYS cc_start: 0.8862 (t) cc_final: 0.8528 (m) REVERT: A 538 ASP cc_start: 0.8081 (t70) cc_final: 0.7404 (t0) REVERT: B 265 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7560 (pp) REVERT: B 304 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: B 354 PHE cc_start: 0.8138 (t80) cc_final: 0.7885 (t80) REVERT: B 394 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 472 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7112 (mtp85) REVERT: B 497 SER cc_start: 0.8153 (m) cc_final: 0.7607 (p) REVERT: B 508 MET cc_start: 0.7419 (mmm) cc_final: 0.6274 (mtp) REVERT: B 538 ASP cc_start: 0.7495 (t0) cc_final: 0.6891 (t0) REVERT: B 577 ILE cc_start: 0.7377 (tt) cc_final: 0.6850 (pt) REVERT: B 608 ASN cc_start: 0.8713 (m-40) cc_final: 0.8498 (m-40) outliers start: 16 outliers final: 10 residues processed: 109 average time/residue: 0.9831 time to fit residues: 114.2558 Evaluate side-chains 110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6796 Z= 0.210 Angle : 0.520 8.681 9202 Z= 0.277 Chirality : 0.040 0.169 986 Planarity : 0.004 0.041 1098 Dihedral : 12.044 60.590 1034 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.36 % Allowed : 15.34 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.67 (0.30), residues: 756 helix: 2.00 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.04 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 573 HIS 0.004 0.001 HIS B 313 PHE 0.015 0.001 PHE B 610 TYR 0.026 0.002 TYR A 496 ARG 0.004 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7828 (mttt) cc_final: 0.7323 (mmtm) REVERT: A 470 THR cc_start: 0.8331 (m) cc_final: 0.7916 (p) REVERT: A 523 CYS cc_start: 0.8882 (t) cc_final: 0.8553 (m) REVERT: A 538 ASP cc_start: 0.8084 (t70) cc_final: 0.7402 (t0) REVERT: A 622 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: B 265 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7553 (pp) REVERT: B 304 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: B 354 PHE cc_start: 0.8149 (t80) cc_final: 0.7903 (t80) REVERT: B 394 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7609 (t80) REVERT: B 472 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7118 (mtp85) REVERT: B 497 SER cc_start: 0.8198 (m) cc_final: 0.7644 (p) REVERT: B 508 MET cc_start: 0.7427 (mmm) cc_final: 0.6278 (mtp) REVERT: B 538 ASP cc_start: 0.7495 (t0) cc_final: 0.6888 (t0) REVERT: B 577 ILE cc_start: 0.7381 (tt) cc_final: 0.6797 (pt) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 1.0949 time to fit residues: 124.3134 Evaluate side-chains 110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6796 Z= 0.200 Angle : 0.516 8.609 9202 Z= 0.276 Chirality : 0.040 0.170 986 Planarity : 0.004 0.041 1098 Dihedral : 11.983 59.638 1034 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 15.19 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 756 helix: 2.02 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.98 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 573 HIS 0.004 0.001 HIS B 313 PHE 0.015 0.001 PHE B 610 TYR 0.025 0.002 TYR B 496 ARG 0.005 0.000 ARG B 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7823 (mttt) cc_final: 0.7319 (mmtm) REVERT: A 470 THR cc_start: 0.8300 (m) cc_final: 0.7885 (p) REVERT: A 523 CYS cc_start: 0.8872 (t) cc_final: 0.8536 (m) REVERT: A 538 ASP cc_start: 0.8080 (t70) cc_final: 0.7402 (t0) REVERT: A 622 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: B 265 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7534 (pp) REVERT: B 304 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: B 354 PHE cc_start: 0.8114 (t80) cc_final: 0.7840 (t80) REVERT: B 394 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7701 (t80) REVERT: B 472 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7149 (mtp85) REVERT: B 497 SER cc_start: 0.8183 (m) cc_final: 0.7663 (p) REVERT: B 508 MET cc_start: 0.7413 (mmm) cc_final: 0.6270 (mtp) REVERT: B 538 ASP cc_start: 0.7498 (t0) cc_final: 0.6893 (t0) REVERT: B 577 ILE cc_start: 0.7385 (tt) cc_final: 0.6814 (pt) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.9906 time to fit residues: 112.1932 Evaluate side-chains 109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.161720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125556 restraints weight = 7162.201| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.49 r_work: 0.3153 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6796 Z= 0.222 Angle : 0.526 8.552 9202 Z= 0.281 Chirality : 0.040 0.168 986 Planarity : 0.004 0.041 1098 Dihedral : 12.005 59.556 1034 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.36 % Allowed : 15.49 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 756 helix: 1.97 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 573 HIS 0.004 0.001 HIS B 313 PHE 0.016 0.002 PHE B 610 TYR 0.024 0.002 TYR B 496 ARG 0.005 0.000 ARG B 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.44 seconds wall clock time: 48 minutes 9.91 seconds (2889.91 seconds total)