Starting phenix.real_space_refine on Wed Sep 17 07:14:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j4x_61138/09_2025/9j4x_61138.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j4x_61138/09_2025/9j4x_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j4x_61138/09_2025/9j4x_61138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j4x_61138/09_2025/9j4x_61138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j4x_61138/09_2025/9j4x_61138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j4x_61138/09_2025/9j4x_61138.map" } resolution = 2.9 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= -0.002 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): 0.01s 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: 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: 1.47, per 1000 atoms: 0.22 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: 0.61 Conformation dependent library (CDL) restraints added in 315.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.14 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: 1.05 Time building geometry restraints manager: 0.77 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: 0.01 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: 1.420 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.240 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: 0.000 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- 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= 0.142 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 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: 0.84 (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 ARG 0.002 0.000 ARG B 611 TYR 0.012 0.001 TYR A 553 PHE 0.015 0.001 PHE B 610 TRP 0.010 0.001 TRP A 395 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6796) covalent geometry : angle 0.51685 ( 9202) hydrogen bonds : bond 0.13758 ( 438) hydrogen bonds : angle 6.18724 ( 1311) *********************** 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 : 0.253 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: 0.5308 time to fit residues: 70.5309 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 : 0.237 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.161587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124186 restraints weight = 7245.003| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.56 r_work: 0.3141 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0953 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= 0.146 Angle : 0.527 7.684 9202 Z= 0.285 Chirality : 0.040 0.178 986 Planarity : 0.004 0.040 1098 Dihedral : 12.398 64.077 1038 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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 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: 1.43 (0.30), residues: 756 helix: 1.97 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.36 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 448 TYR 0.017 0.002 TYR A 352 PHE 0.022 0.002 PHE B 511 TRP 0.012 0.002 TRP A 395 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6796) covalent geometry : angle 0.52683 ( 9202) hydrogen bonds : bond 0.04889 ( 438) hydrogen bonds : angle 4.42801 ( 1311) *********************** 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 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.249 Fit side-chains REVERT: A 376 LYS cc_start: 0.7878 (mttt) cc_final: 0.7402 (mmtm) REVERT: A 471 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7909 (mmtm) REVERT: A 523 CYS cc_start: 0.8851 (t) cc_final: 0.8531 (m) REVERT: A 538 ASP cc_start: 0.8220 (t70) cc_final: 0.7617 (t0) REVERT: A 622 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7945 (mt-10) REVERT: B 265 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7718 (pp) REVERT: B 394 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 497 SER cc_start: 0.8337 (m) cc_final: 0.8023 (p) REVERT: B 508 MET cc_start: 0.7707 (mmm) cc_final: 0.6538 (mtp) REVERT: B 538 ASP cc_start: 0.7716 (t0) cc_final: 0.7170 (t0) REVERT: B 549 GLU cc_start: 0.8441 (tt0) cc_final: 0.8206 (tt0) REVERT: B 550 GLU cc_start: 0.7057 (pt0) cc_final: 0.6596 (pm20) REVERT: B 577 ILE cc_start: 0.7415 (tt) cc_final: 0.7059 (pt) REVERT: B 608 ASN cc_start: 0.8710 (m-40) cc_final: 0.8471 (m110) outliers start: 15 outliers final: 4 residues processed: 119 average time/residue: 0.4579 time to fit residues: 57.8793 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 576 GLN B 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122533 restraints weight = 7153.686| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.58 r_work: 0.3129 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1192 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= 0.140 Angle : 0.513 7.034 9202 Z= 0.276 Chirality : 0.040 0.176 986 Planarity : 0.004 0.036 1098 Dihedral : 12.265 63.171 1036 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.21 % Allowed : 13.27 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.56 (0.30), residues: 756 helix: 2.05 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.024 0.002 TYR A 496 PHE 0.015 0.001 PHE B 511 TRP 0.014 0.002 TRP A 395 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6796) covalent geometry : angle 0.51273 ( 9202) hydrogen bonds : bond 0.04613 ( 438) hydrogen bonds : angle 4.24819 ( 1311) *********************** 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 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.290 Fit side-chains REVERT: A 376 LYS cc_start: 0.7874 (mttt) cc_final: 0.7393 (mmtm) REVERT: A 471 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7937 (mmtm) REVERT: A 523 CYS cc_start: 0.8908 (t) cc_final: 0.8570 (m) REVERT: A 538 ASP cc_start: 0.8260 (t70) cc_final: 0.7659 (t0) REVERT: A 622 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7878 (mt-10) REVERT: B 265 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7672 (pp) REVERT: B 497 SER cc_start: 0.8415 (m) cc_final: 0.7893 (p) REVERT: B 508 MET cc_start: 0.7692 (mmm) cc_final: 0.6528 (mtp) REVERT: B 538 ASP cc_start: 0.7733 (t0) cc_final: 0.7206 (t0) REVERT: B 549 GLU cc_start: 0.8402 (tt0) cc_final: 0.8145 (tt0) REVERT: B 550 GLU cc_start: 0.7118 (pt0) cc_final: 0.6732 (pm20) REVERT: B 577 ILE cc_start: 0.7555 (tt) cc_final: 0.7106 (pt) REVERT: B 608 ASN cc_start: 0.8699 (m-40) cc_final: 0.8454 (m110) outliers start: 15 outliers final: 5 residues processed: 113 average time/residue: 0.4791 time to fit residues: 57.5433 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 : 0.251 ------------------------------------------------------------------------------- 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 447 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 7 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.161668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126012 restraints weight = 7195.744| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.46 r_work: 0.3161 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1302 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= 0.141 Angle : 0.513 6.805 9202 Z= 0.275 Chirality : 0.040 0.175 986 Planarity : 0.004 0.038 1098 Dihedral : 12.181 63.304 1034 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.06 % Allowed : 13.72 % 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 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: 1.60 (0.30), residues: 756 helix: 2.09 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.023 0.002 TYR A 496 PHE 0.015 0.001 PHE B 610 TRP 0.013 0.002 TRP A 395 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6796) covalent geometry : angle 0.51254 ( 9202) hydrogen bonds : bond 0.04530 ( 438) hydrogen bonds : angle 4.16907 ( 1311) *********************** 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 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.299 Fit side-chains REVERT: A 376 LYS cc_start: 0.7792 (mttt) cc_final: 0.7294 (mmtm) REVERT: A 394 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7749 (t80) REVERT: A 470 THR cc_start: 0.8445 (m) cc_final: 0.8035 (p) REVERT: A 471 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7886 (mmtt) REVERT: A 523 CYS cc_start: 0.8880 (t) cc_final: 0.8523 (m) REVERT: B 265 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7675 (pp) REVERT: B 472 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6981 (mtp85) REVERT: B 497 SER cc_start: 0.8379 (m) cc_final: 0.7833 (p) REVERT: B 508 MET cc_start: 0.7581 (mmm) cc_final: 0.6408 (mtp) REVERT: B 538 ASP cc_start: 0.7681 (t0) cc_final: 0.7142 (t0) REVERT: B 549 GLU cc_start: 0.8358 (tt0) cc_final: 0.8085 (tt0) REVERT: B 550 GLU cc_start: 0.7073 (pt0) cc_final: 0.6661 (pm20) REVERT: B 577 ILE cc_start: 0.7565 (tt) cc_final: 0.7112 (pt) REVERT: B 608 ASN cc_start: 0.8654 (m-40) cc_final: 0.8404 (m110) outliers start: 14 outliers final: 7 residues processed: 119 average time/residue: 0.4744 time to fit residues: 59.9786 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.161772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125507 restraints weight = 7268.424| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.50 r_work: 0.3144 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6796 Z= 0.149 Angle : 0.527 8.468 9202 Z= 0.279 Chirality : 0.041 0.176 986 Planarity : 0.004 0.039 1098 Dihedral : 12.223 63.475 1034 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.95 % Allowed : 14.01 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 756 helix: 2.04 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.026 0.002 TYR A 496 PHE 0.016 0.002 PHE B 391 TRP 0.013 0.002 TRP A 395 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6796) covalent geometry : angle 0.52678 ( 9202) hydrogen bonds : bond 0.04553 ( 438) hydrogen bonds : angle 4.18120 ( 1311) *********************** 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 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 354 PHE cc_start: 0.7357 (t80) cc_final: 0.7111 (t80) REVERT: A 376 LYS cc_start: 0.7797 (mttt) cc_final: 0.7285 (mmtm) REVERT: A 394 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7774 (t80) REVERT: A 470 THR cc_start: 0.8449 (m) cc_final: 0.8034 (p) REVERT: A 471 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7887 (mmtt) REVERT: A 523 CYS cc_start: 0.8878 (t) cc_final: 0.8520 (m) REVERT: A 538 ASP cc_start: 0.8225 (t70) cc_final: 0.7602 (t0) REVERT: A 622 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: B 265 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 394 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 472 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7025 (mtp85) REVERT: B 497 SER cc_start: 0.8376 (m) cc_final: 0.7816 (p) REVERT: B 508 MET cc_start: 0.7621 (mmm) cc_final: 0.6429 (mtp) REVERT: B 538 ASP cc_start: 0.7703 (t0) cc_final: 0.7149 (t0) REVERT: B 549 GLU cc_start: 0.8366 (tt0) cc_final: 0.8061 (tt0) REVERT: B 550 GLU cc_start: 0.7073 (pt0) cc_final: 0.6626 (pm20) REVERT: B 577 ILE cc_start: 0.7583 (tt) cc_final: 0.7092 (pt) REVERT: B 608 ASN cc_start: 0.8672 (m-40) cc_final: 0.8435 (m110) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.4452 time to fit residues: 55.5728 Evaluate side-chains 112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 394 PHE 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 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 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 43 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.158754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121208 restraints weight = 7290.883| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.58 r_work: 0.3098 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6796 Z= 0.172 Angle : 0.547 8.386 9202 Z= 0.289 Chirality : 0.042 0.208 986 Planarity : 0.004 0.040 1098 Dihedral : 12.393 64.475 1034 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.65 % Allowed : 14.01 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.48 (0.30), residues: 756 helix: 1.96 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.027 0.002 TYR A 496 PHE 0.016 0.002 PHE A 605 TRP 0.012 0.002 TRP A 514 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6796) covalent geometry : angle 0.54732 ( 9202) hydrogen bonds : bond 0.04740 ( 438) hydrogen bonds : angle 4.23615 ( 1311) *********************** 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 119 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7914 (mttt) cc_final: 0.7429 (mmtm) REVERT: A 394 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 470 THR cc_start: 0.8452 (m) cc_final: 0.8056 (p) REVERT: A 471 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7950 (mmtt) REVERT: A 523 CYS cc_start: 0.8941 (t) cc_final: 0.8583 (m) REVERT: A 538 ASP cc_start: 0.8301 (t70) cc_final: 0.7600 (t0) REVERT: A 622 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: B 265 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7685 (pp) REVERT: B 394 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7789 (t80) REVERT: B 472 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7038 (mtp85) REVERT: B 497 SER cc_start: 0.8397 (m) cc_final: 0.7840 (p) REVERT: B 508 MET cc_start: 0.7699 (mmm) cc_final: 0.6485 (mtp) REVERT: B 538 ASP cc_start: 0.7737 (t0) cc_final: 0.7169 (t0) REVERT: B 549 GLU cc_start: 0.8453 (tt0) cc_final: 0.8136 (tt0) REVERT: B 550 GLU cc_start: 0.7143 (pt0) cc_final: 0.6671 (pm20) REVERT: B 577 ILE cc_start: 0.7670 (tt) cc_final: 0.7127 (pt) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.4481 time to fit residues: 53.6132 Evaluate side-chains 113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 394 PHE 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 A residue 622 GLU 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 551 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.160948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123713 restraints weight = 7195.190| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.57 r_work: 0.3131 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1525 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= 0.133 Angle : 0.513 8.315 9202 Z= 0.274 Chirality : 0.040 0.197 986 Planarity : 0.004 0.041 1098 Dihedral : 12.176 62.464 1034 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.06 % Allowed : 14.75 % 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 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: 1.64 (0.30), residues: 756 helix: 2.10 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.029 0.002 TYR A 496 PHE 0.016 0.001 PHE B 610 TRP 0.017 0.002 TRP A 573 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6796) covalent geometry : angle 0.51322 ( 9202) hydrogen bonds : bond 0.04416 ( 438) hydrogen bonds : angle 4.13558 ( 1311) *********************** 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 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7868 (mttt) cc_final: 0.7392 (mmtm) REVERT: A 470 THR cc_start: 0.8405 (m) cc_final: 0.8044 (p) REVERT: A 523 CYS cc_start: 0.8919 (t) cc_final: 0.8566 (m) REVERT: A 538 ASP cc_start: 0.8289 (t70) cc_final: 0.7581 (t0) REVERT: A 622 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: B 265 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7678 (pp) REVERT: B 394 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 472 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7161 (mtp85) REVERT: B 497 SER cc_start: 0.8356 (m) cc_final: 0.7771 (p) REVERT: B 508 MET cc_start: 0.7631 (mmm) cc_final: 0.6441 (mtp) REVERT: B 538 ASP cc_start: 0.7725 (t0) cc_final: 0.7151 (t0) REVERT: B 577 ILE cc_start: 0.7616 (tt) cc_final: 0.7156 (pt) REVERT: B 608 ASN cc_start: 0.8727 (m-40) cc_final: 0.8526 (m-40) outliers start: 14 outliers final: 5 residues processed: 113 average time/residue: 0.4840 time to fit residues: 58.1694 Evaluate side-chains 111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 497 SER 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 341 VAL Chi-restraints excluded: chain B residue 394 PHE 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 29 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.162541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126421 restraints weight = 7210.259| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.49 r_work: 0.3156 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1578 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= 0.138 Angle : 0.517 8.192 9202 Z= 0.276 Chirality : 0.040 0.224 986 Planarity : 0.004 0.041 1098 Dihedral : 12.122 61.736 1034 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.92 % Allowed : 15.19 % 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 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: 1.63 (0.30), residues: 756 helix: 1.99 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.028 0.002 TYR A 496 PHE 0.016 0.001 PHE B 610 TRP 0.019 0.002 TRP A 573 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6796) covalent geometry : angle 0.51696 ( 9202) hydrogen bonds : bond 0.04425 ( 438) hydrogen bonds : angle 4.13582 ( 1311) *********************** 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 115 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7792 (mttt) cc_final: 0.7300 (mmtm) REVERT: A 470 THR cc_start: 0.8377 (m) cc_final: 0.7930 (p) REVERT: A 523 CYS cc_start: 0.8854 (t) cc_final: 0.8485 (m) REVERT: A 529 ASP cc_start: 0.8294 (m-30) cc_final: 0.7887 (m-30) REVERT: A 622 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: B 265 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7708 (pp) REVERT: B 394 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 472 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7127 (mtp85) REVERT: B 497 SER cc_start: 0.8304 (m) cc_final: 0.7712 (p) REVERT: B 508 MET cc_start: 0.7574 (mmm) cc_final: 0.6408 (mtp) REVERT: B 538 ASP cc_start: 0.7669 (t0) cc_final: 0.7095 (t0) REVERT: B 577 ILE cc_start: 0.7553 (tt) cc_final: 0.7029 (pt) outliers start: 13 outliers final: 8 residues processed: 109 average time/residue: 0.4792 time to fit residues: 55.6380 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 : 0.243 ------------------------------------------------------------------------------- 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 A residue 622 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 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 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 33 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.162219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126173 restraints weight = 7244.515| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.56 r_work: 0.3173 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1633 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= 0.137 Angle : 0.516 8.086 9202 Z= 0.276 Chirality : 0.040 0.171 986 Planarity : 0.004 0.041 1098 Dihedral : 12.064 60.679 1034 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.77 % Allowed : 15.19 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.64 (0.30), residues: 756 helix: 1.98 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.04 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.027 0.002 TYR B 496 PHE 0.017 0.001 PHE B 610 TRP 0.023 0.002 TRP A 573 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6796) covalent geometry : angle 0.51619 ( 9202) hydrogen bonds : bond 0.04400 ( 438) hydrogen bonds : angle 4.12931 ( 1311) *********************** 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 113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7782 (mttt) cc_final: 0.7285 (mmtm) REVERT: A 413 MET cc_start: 0.7803 (mtp) cc_final: 0.7412 (ttt) REVERT: A 470 THR cc_start: 0.8358 (m) cc_final: 0.7914 (p) REVERT: A 523 CYS cc_start: 0.8873 (t) cc_final: 0.8506 (m) REVERT: A 529 ASP cc_start: 0.8291 (m-30) cc_final: 0.7928 (m-30) REVERT: B 265 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7659 (pp) REVERT: B 394 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7827 (t80) REVERT: B 472 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7172 (mtp85) REVERT: B 497 SER cc_start: 0.8353 (m) cc_final: 0.7756 (p) REVERT: B 508 MET cc_start: 0.7511 (mmm) cc_final: 0.6340 (mtp) REVERT: B 538 ASP cc_start: 0.7670 (t0) cc_final: 0.7097 (t0) REVERT: B 577 ILE cc_start: 0.7565 (tt) cc_final: 0.7064 (pt) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.4726 time to fit residues: 53.9248 Evaluate side-chains 108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 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 75 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 0.0870 chunk 45 optimal weight: 0.0370 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.164876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129211 restraints weight = 7211.032| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.49 r_work: 0.3215 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6796 Z= 0.117 Angle : 0.498 8.075 9202 Z= 0.268 Chirality : 0.039 0.173 986 Planarity : 0.004 0.040 1098 Dihedral : 11.826 59.060 1034 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.62 % Allowed : 15.63 % 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 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: 1.76 (0.31), residues: 756 helix: 2.06 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.97 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.024 0.002 TYR A 496 PHE 0.017 0.001 PHE B 610 TRP 0.023 0.002 TRP A 573 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6796) covalent geometry : angle 0.49766 ( 9202) hydrogen bonds : bond 0.04150 ( 438) hydrogen bonds : angle 4.06329 ( 1311) ********************** 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 113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8752 (t80) cc_final: 0.8514 (t80) REVERT: A 376 LYS cc_start: 0.7722 (mttt) cc_final: 0.7250 (mmtm) REVERT: A 413 MET cc_start: 0.7791 (mtp) cc_final: 0.7441 (ttt) REVERT: A 470 THR cc_start: 0.8326 (m) cc_final: 0.7899 (p) REVERT: A 523 CYS cc_start: 0.8808 (t) cc_final: 0.8469 (m) REVERT: A 529 ASP cc_start: 0.8216 (m-30) cc_final: 0.7829 (m-30) REVERT: A 622 GLU cc_start: 0.8140 (mp0) cc_final: 0.7914 (mt-10) REVERT: B 265 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7646 (pp) REVERT: B 394 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 417 TYR cc_start: 0.7867 (m-10) cc_final: 0.7554 (m-80) REVERT: B 472 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7158 (mtp85) REVERT: B 497 SER cc_start: 0.8186 (m) cc_final: 0.7755 (p) REVERT: B 508 MET cc_start: 0.7465 (mmm) cc_final: 0.6346 (mtp) REVERT: B 538 ASP cc_start: 0.7688 (t0) cc_final: 0.7139 (t0) REVERT: B 577 ILE cc_start: 0.7588 (tt) cc_final: 0.7138 (pt) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.4640 time to fit residues: 53.1754 Evaluate side-chains 104 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.160423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124099 restraints weight = 7198.647| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.49 r_work: 0.3138 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6796 Z= 0.158 Angle : 0.538 7.981 9202 Z= 0.287 Chirality : 0.040 0.168 986 Planarity : 0.004 0.041 1098 Dihedral : 12.005 59.885 1034 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.47 % Allowed : 15.49 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.63 (0.30), residues: 756 helix: 1.95 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.95 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.024 0.002 TYR B 496 PHE 0.016 0.002 PHE B 610 TRP 0.029 0.002 TRP A 573 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6796) covalent geometry : angle 0.53818 ( 9202) hydrogen bonds : bond 0.04507 ( 438) hydrogen bonds : angle 4.17602 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.34 seconds wall clock time: 42 minutes 48.06 seconds (2568.06 seconds total)