Starting phenix.real_space_refine on Wed Oct 9 18:16:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5u_19750/10_2024/8s5u_19750.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5u_19750/10_2024/8s5u_19750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5u_19750/10_2024/8s5u_19750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5u_19750/10_2024/8s5u_19750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5u_19750/10_2024/8s5u_19750.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5u_19750/10_2024/8s5u_19750.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2652 2.51 5 N 620 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3998 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "A" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2984 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'NAG': 1, 'VIB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.14, per 1000 atoms: 1.04 Number of scatterers: 3998 At special positions: 0 Unit cell: (107.1, 72.25, 64.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 706 8.00 N 620 7.00 C 2652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 45 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 484.5 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 3 sheets defined 66.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.728A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.503A pdb=" N THR B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'A' and resid 12 through 28 removed outlier: 3.721A pdb=" N THR A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.884A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 78 through 99 removed outlier: 4.364A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.504A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.540A pdb=" N ARG A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.805A pdb=" N LEU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 removed outlier: 4.120A pdb=" N SER A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.505A pdb=" N GLN A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.571A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.757A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.529A pdb=" N CYS A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.267A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.896A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.371A pdb=" N VAL B 12 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.371A pdb=" N VAL B 12 " --> pdb=" O SER B 127 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 753 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: 1.21 Time building geometry restraints manager: 1.16 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: 630 1.32 - 1.44: 1220 1.44 - 1.56: 2225 1.56 - 1.68: 1 1.68 - 1.81: 32 Bond restraints: 4108 Sorted by residual: bond pdb=" C5 VIB A 602 " pdb=" S1 VIB A 602 " ideal model delta sigma weight residual 1.721 1.508 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C4 VIB A 602 " pdb=" N3 VIB A 602 " ideal model delta sigma weight residual 1.385 1.572 -0.187 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C2A VIB A 602 " pdb=" N3A VIB A 602 " ideal model delta sigma weight residual 1.323 1.478 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C2A VIB A 602 " pdb=" N1A VIB A 602 " ideal model delta sigma weight residual 1.331 1.481 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C2 VIB A 602 " pdb=" S1 VIB A 602 " ideal model delta sigma weight residual 1.670 1.539 0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 4103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 5562 3.33 - 6.67: 40 6.67 - 10.00: 1 10.00 - 13.34: 0 13.34 - 16.67: 1 Bond angle restraints: 5604 Sorted by residual: angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 112.34 120.30 -7.96 1.30e+00 5.92e-01 3.75e+01 angle pdb=" C2 VIB A 602 " pdb=" S1 VIB A 602 " pdb=" C5 VIB A 602 " ideal model delta sigma weight residual 91.25 107.92 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" N LEU A 95 " pdb=" CA LEU A 95 " pdb=" C LEU A 95 " ideal model delta sigma weight residual 113.23 107.31 5.92 1.24e+00 6.50e-01 2.28e+01 angle pdb=" N SER A 353 " pdb=" CA SER A 353 " pdb=" C SER A 353 " ideal model delta sigma weight residual 112.90 107.37 5.53 1.31e+00 5.83e-01 1.78e+01 angle pdb=" N LEU A 97 " pdb=" CA LEU A 97 " pdb=" C LEU A 97 " ideal model delta sigma weight residual 112.23 106.92 5.31 1.26e+00 6.30e-01 1.77e+01 ... (remaining 5599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2015 15.89 - 31.78: 247 31.78 - 47.68: 73 47.68 - 63.57: 14 63.57 - 79.46: 6 Dihedral angle restraints: 2355 sinusoidal: 880 harmonic: 1475 Sorted by residual: dihedral pdb=" CA TYR A 126 " pdb=" C TYR A 126 " pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG ARG A 402 " pdb=" CD ARG A 402 " pdb=" NE ARG A 402 " pdb=" CZ ARG A 402 " ideal model delta sinusoidal sigma weight residual 90.00 133.07 -43.07 2 1.50e+01 4.44e-03 9.95e+00 dihedral pdb=" CA LYS A 306 " pdb=" CB LYS A 306 " pdb=" CG LYS A 306 " pdb=" CD LYS A 306 " ideal model delta sinusoidal sigma weight residual -180.00 -121.08 -58.92 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 478 0.044 - 0.088: 133 0.088 - 0.133: 23 0.133 - 0.177: 5 0.177 - 0.221: 3 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA TYR A 273 " pdb=" N TYR A 273 " pdb=" C TYR A 273 " pdb=" CB TYR A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA TYR A 79 " pdb=" N TYR A 79 " pdb=" C TYR A 79 " pdb=" CB TYR A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 639 not shown) Planarity restraints: 682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.359 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A 601 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 80 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 81 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 352 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C PHE A 352 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 352 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 353 " 0.009 2.00e-02 2.50e+03 ... (remaining 679 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1493 2.85 - 3.36: 3830 3.36 - 3.88: 6459 3.88 - 4.39: 7731 4.39 - 4.90: 13382 Nonbonded interactions: 32895 Sorted by model distance: nonbonded pdb=" OG1 THR B 106 " pdb=" OD2 ASP A 304 " model vdw 2.338 3.040 nonbonded pdb=" O LEU A 377 " pdb=" OG SER A 381 " model vdw 2.394 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OD1 ASP A 311 " model vdw 2.402 3.040 nonbonded pdb=" O ARG B 31 " pdb=" O PRO B 102 " model vdw 2.404 3.040 nonbonded pdb=" O SER B 117 " pdb=" OG SER B 117 " model vdw 2.408 3.040 ... (remaining 32890 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.009 0.213 4108 Z= 0.547 Angle : 0.708 16.670 5604 Z= 0.414 Chirality : 0.043 0.221 642 Planarity : 0.012 0.306 681 Dihedral : 15.772 79.460 1412 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.47 % Allowed : 17.73 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.38), residues: 496 helix: 0.13 (0.30), residues: 290 sheet: -1.03 (0.78), residues: 46 loop : -1.07 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.026 0.001 PHE A 71 TYR 0.008 0.001 TYR A 171 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.514 Fit side-chains REVERT: A 75 ASP cc_start: 0.8172 (m-30) cc_final: 0.7907 (m-30) REVERT: A 421 MET cc_start: 0.7598 (ttp) cc_final: 0.7123 (ttp) outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.1803 time to fit residues: 15.7171 Evaluate side-chains 60 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN A 340 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4108 Z= 0.198 Angle : 0.536 5.560 5604 Z= 0.291 Chirality : 0.041 0.140 642 Planarity : 0.005 0.063 681 Dihedral : 5.981 59.072 575 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.89 % Allowed : 18.68 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.38), residues: 496 helix: 1.18 (0.30), residues: 300 sheet: -0.70 (0.75), residues: 46 loop : -0.66 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.018 0.001 PHE A 90 TYR 0.012 0.001 TYR A 445 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.412 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 70 average time/residue: 0.1163 time to fit residues: 11.0391 Evaluate side-chains 55 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 12 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.1856 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4108 Z= 0.153 Angle : 0.473 5.589 5604 Z= 0.259 Chirality : 0.040 0.133 642 Planarity : 0.004 0.061 681 Dihedral : 5.408 59.185 575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.36 % Allowed : 19.62 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 496 helix: 1.77 (0.30), residues: 300 sheet: -0.31 (0.75), residues: 46 loop : -0.32 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.016 0.001 PHE A 71 TYR 0.015 0.001 TYR A 14 ARG 0.001 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.503 Fit side-chains REVERT: A 455 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5266 (ttp) outliers start: 10 outliers final: 3 residues processed: 60 average time/residue: 0.1449 time to fit residues: 12.0223 Evaluate side-chains 56 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.7958 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4108 Z= 0.214 Angle : 0.491 5.818 5604 Z= 0.268 Chirality : 0.041 0.133 642 Planarity : 0.004 0.059 681 Dihedral : 5.306 58.682 575 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 21.04 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.39), residues: 496 helix: 1.84 (0.30), residues: 301 sheet: -0.13 (0.73), residues: 46 loop : -0.24 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.020 0.002 PHE A 71 TYR 0.022 0.001 TYR A 14 ARG 0.001 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.395 Fit side-chains REVERT: A 363 MET cc_start: 0.8840 (mtm) cc_final: 0.8637 (ttp) REVERT: A 455 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5312 (ttp) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.1185 time to fit residues: 10.0192 Evaluate side-chains 58 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4108 Z= 0.307 Angle : 0.544 5.997 5604 Z= 0.294 Chirality : 0.043 0.145 642 Planarity : 0.004 0.056 681 Dihedral : 5.393 57.988 575 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 22.70 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.39), residues: 496 helix: 1.73 (0.30), residues: 301 sheet: -0.22 (0.73), residues: 46 loop : -0.39 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.024 0.002 PHE A 71 TYR 0.013 0.001 TYR A 445 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.445 Fit side-chains REVERT: A 455 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5244 (ttp) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1268 time to fit residues: 10.8999 Evaluate side-chains 62 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4108 Z= 0.284 Angle : 0.531 5.984 5604 Z= 0.288 Chirality : 0.043 0.145 642 Planarity : 0.004 0.054 681 Dihedral : 5.295 53.553 575 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 22.22 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.39), residues: 496 helix: 1.72 (0.30), residues: 300 sheet: -0.25 (0.73), residues: 46 loop : -0.33 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.023 0.002 PHE A 71 TYR 0.013 0.001 TYR A 280 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.447 Fit side-chains REVERT: A 363 MET cc_start: 0.8893 (mtm) cc_final: 0.8623 (ttp) REVERT: A 415 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8722 (tt) REVERT: A 455 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5303 (ttp) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.1452 time to fit residues: 12.5902 Evaluate side-chains 65 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4108 Z= 0.209 Angle : 0.512 6.423 5604 Z= 0.278 Chirality : 0.041 0.137 642 Planarity : 0.004 0.053 681 Dihedral : 5.133 49.995 575 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.84 % Allowed : 22.46 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.39), residues: 496 helix: 1.88 (0.30), residues: 300 sheet: -0.16 (0.74), residues: 46 loop : -0.24 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.018 0.001 PHE A 71 TYR 0.012 0.001 TYR A 280 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.377 Fit side-chains REVERT: A 74 THR cc_start: 0.8191 (m) cc_final: 0.7813 (m) REVERT: A 455 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5195 (ttp) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.1247 time to fit residues: 10.6372 Evaluate side-chains 61 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4108 Z= 0.313 Angle : 0.558 6.414 5604 Z= 0.298 Chirality : 0.043 0.146 642 Planarity : 0.004 0.053 681 Dihedral : 5.236 47.263 575 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.13 % Allowed : 22.70 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.39), residues: 496 helix: 1.73 (0.30), residues: 301 sheet: -0.17 (0.75), residues: 44 loop : -0.40 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.024 0.002 PHE A 71 TYR 0.016 0.002 TYR A 280 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.395 Fit side-chains REVERT: A 455 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5096 (ttp) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.1428 time to fit residues: 12.3113 Evaluate side-chains 66 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4108 Z= 0.264 Angle : 0.543 6.812 5604 Z= 0.291 Chirality : 0.043 0.144 642 Planarity : 0.004 0.052 681 Dihedral : 5.180 46.881 575 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.36 % Allowed : 22.22 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.39), residues: 496 helix: 1.79 (0.30), residues: 301 sheet: -0.32 (0.74), residues: 46 loop : -0.39 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.021 0.002 PHE A 71 TYR 0.014 0.001 TYR A 280 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.516 Fit side-chains REVERT: A 455 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4998 (ttp) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1512 time to fit residues: 12.7768 Evaluate side-chains 63 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4108 Z= 0.295 Angle : 0.557 7.240 5604 Z= 0.297 Chirality : 0.043 0.147 642 Planarity : 0.004 0.052 681 Dihedral : 5.240 47.168 575 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.36 % Allowed : 22.22 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.39), residues: 496 helix: 1.74 (0.30), residues: 301 sheet: -0.36 (0.74), residues: 46 loop : -0.44 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.022 0.002 PHE A 71 TYR 0.014 0.001 TYR A 280 ARG 0.002 0.000 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.473 Fit side-chains REVERT: A 455 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.4899 (ttp) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.1539 time to fit residues: 12.5873 Evaluate side-chains 61 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.129059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116329 restraints weight = 5074.190| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.39 r_work: 0.3102 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4108 Z= 0.213 Angle : 0.533 7.425 5604 Z= 0.283 Chirality : 0.041 0.140 642 Planarity : 0.004 0.051 681 Dihedral : 5.108 47.395 575 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.42 % Allowed : 23.17 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.39), residues: 496 helix: 1.91 (0.31), residues: 301 sheet: -0.29 (0.74), residues: 46 loop : -0.32 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.018 0.001 PHE A 71 TYR 0.015 0.001 TYR A 280 ARG 0.002 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.28 seconds wall clock time: 28 minutes 30.29 seconds (1710.29 seconds total)