Starting phenix.real_space_refine on Wed Feb 12 22:44:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl1_60215/02_2025/8zl1_60215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl1_60215/02_2025/8zl1_60215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl1_60215/02_2025/8zl1_60215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl1_60215/02_2025/8zl1_60215.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl1_60215/02_2025/8zl1_60215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl1_60215/02_2025/8zl1_60215.cif" } resolution = 2.86 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= 0.004 sd= 0.017 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 2 5.49 5 S 88 5.16 5 C 5624 2.51 5 N 1328 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.49, per 1000 atoms: 0.65 Number of scatterers: 8466 At special positions: 0 Unit cell: (86.7825, 97.527, 105.792, 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 88 16.00 P 2 15.00 O 1424 8.00 N 1328 7.00 C 5624 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 33 through 60 removed outlier: 3.629A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Proline residue: A 50 - end of helix Proline residue: A 55 - end of helix removed outlier: 3.654A pdb=" N ASN A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 81 Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.757A pdb=" N ILE A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.659A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.554A pdb=" N CYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.624A pdb=" N ARG A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 238 Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.643A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.789A pdb=" N GLU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.398A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 423 through 442 removed outlier: 4.238A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.081A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 479 through 498 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.865A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 544 through 567 removed outlier: 4.926A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 40 through 59 Proline residue: B 50 - end of helix Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.649A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 100 removed outlier: 4.095A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.592A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.501A pdb=" N CYS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.609A pdb=" N ARG B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 191 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 239 through 240 No H-bonds generated for 'chain 'B' and resid 239 through 240' Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.661A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 296 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 316 through 329 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.960A pdb=" N THR B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 423 through 442 removed outlier: 4.222A pdb=" N PHE B 427 " --> pdb=" O TRP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 454 removed outlier: 4.224A pdb=" N GLY B 454 " --> pdb=" O ASN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.970A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 523 through 533 Processing helix chain 'B' and resid 536 through 567 removed outlier: 3.507A pdb=" N MET B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 4.757A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 562 hydrogen bonds defined for protein. 1674 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: 2.51 Time building geometry restraints manager: 2.57 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: 1297 1.32 - 1.44: 2274 1.44 - 1.57: 4967 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 8688 Sorted by residual: bond pdb=" N SER B 302 " pdb=" CA SER B 302 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.58e+00 bond pdb=" N MET B 295 " pdb=" CA MET B 295 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" N GLU B 307 " pdb=" CA GLU B 307 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.87e+00 ... (remaining 8683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11616 2.33 - 4.66: 168 4.66 - 6.99: 24 6.99 - 9.32: 1 9.32 - 11.65: 1 Bond angle restraints: 11810 Sorted by residual: angle pdb=" N GLU B 304 " pdb=" CA GLU B 304 " pdb=" C GLU B 304 " ideal model delta sigma weight residual 113.30 107.06 6.24 1.34e+00 5.57e-01 2.17e+01 angle pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O14 PTY B 601 " ideal model delta sigma weight residual 92.90 104.55 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA SER B 302 " pdb=" C SER B 302 " pdb=" O SER B 302 " ideal model delta sigma weight residual 121.23 117.13 4.10 1.07e+00 8.73e-01 1.47e+01 angle pdb=" N GLN B 309 " pdb=" CA GLN B 309 " pdb=" C GLN B 309 " ideal model delta sigma weight residual 110.97 107.09 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" O LYS A 260 " ideal model delta sigma weight residual 121.46 117.34 4.12 1.17e+00 7.31e-01 1.24e+01 ... (remaining 11805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.01: 4971 26.01 - 52.02: 166 52.02 - 78.04: 9 78.04 - 104.05: 0 104.05 - 130.06: 4 Dihedral angle restraints: 5150 sinusoidal: 2026 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ARG A 371 " pdb=" C ARG A 371 " pdb=" N ASN A 372 " pdb=" CA ASN A 372 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" N1 PTY B 601 " pdb=" C2 PTY B 601 " pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " ideal model delta sinusoidal sigma weight residual 65.33 -64.73 130.06 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual 300.23 176.96 123.27 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1072 0.052 - 0.104: 263 0.104 - 0.155: 32 0.155 - 0.207: 8 0.207 - 0.259: 1 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C6 PTY B 601 " pdb=" C1 PTY B 601 " pdb=" C5 PTY B 601 " pdb=" O7 PTY B 601 " both_signs ideal model delta sigma weight residual False 2.49 2.23 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA LYS A 260 " pdb=" N LYS A 260 " pdb=" C LYS A 260 " pdb=" CB LYS A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA VAL B 308 " pdb=" N VAL B 308 " pdb=" C VAL B 308 " pdb=" CB VAL B 308 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1373 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 559 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C CYS A 559 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 559 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 560 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 559 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C CYS B 559 " -0.037 2.00e-02 2.50e+03 pdb=" O CYS B 559 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 560 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 54 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 55 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.029 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1118 2.75 - 3.29: 8911 3.29 - 3.83: 14599 3.83 - 4.36: 16814 4.36 - 4.90: 29014 Nonbonded interactions: 70456 Sorted by model distance: nonbonded pdb=" O MET B 279 " pdb=" OG1 THR B 283 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" OG1 THR A 376 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 348 " pdb=" OG1 THR A 352 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 373 " pdb=" OG SER B 104 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR B 475 " pdb=" OD1 ASN B 480 " model vdw 2.340 3.040 ... (remaining 70451 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: 0.04 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: 0.670 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.350 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.004 0.046 8688 Z= 0.270 Angle : 0.653 11.651 11810 Z= 0.366 Chirality : 0.044 0.259 1376 Planarity : 0.005 0.052 1440 Dihedral : 12.593 130.060 3138 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.22 % Allowed : 0.11 % Favored : 99.67 % 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: 1.27 (0.25), residues: 1070 helix: 1.41 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.020 0.001 PHE A 251 TYR 0.027 0.001 TYR B 111 ARG 0.010 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.941 Fit side-chains REVERT: A 323 ASP cc_start: 0.9217 (t70) cc_final: 0.8827 (p0) REVERT: A 340 MET cc_start: 0.9323 (ttm) cc_final: 0.9080 (ttm) REVERT: A 349 MET cc_start: 0.9171 (mmm) cc_final: 0.8869 (mmm) REVERT: B 267 ASP cc_start: 0.8221 (t0) cc_final: 0.7944 (t0) REVERT: B 363 ASP cc_start: 0.9073 (m-30) cc_final: 0.8855 (m-30) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 1.4096 time to fit residues: 119.9046 Evaluate side-chains 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050381 restraints weight = 27086.949| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.28 r_work: 0.2741 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8688 Z= 0.182 Angle : 0.564 6.730 11810 Z= 0.291 Chirality : 0.041 0.162 1376 Planarity : 0.005 0.047 1440 Dihedral : 8.380 113.057 1226 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 5.51 % Favored : 93.61 % 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: 1.28 (0.25), residues: 1070 helix: 1.40 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.026 0.001 PHE A 251 TYR 0.034 0.001 TYR A 282 ARG 0.008 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.929 Fit side-chains REVERT: A 323 ASP cc_start: 0.9319 (t70) cc_final: 0.8899 (p0) REVERT: A 332 MET cc_start: 0.8108 (ttm) cc_final: 0.7749 (ttp) REVERT: A 340 MET cc_start: 0.9273 (ttm) cc_final: 0.9054 (ttm) REVERT: A 349 MET cc_start: 0.9285 (mmm) cc_final: 0.8953 (mmm) REVERT: B 267 ASP cc_start: 0.8161 (t0) cc_final: 0.7873 (t0) REVERT: B 363 ASP cc_start: 0.9137 (m-30) cc_final: 0.8902 (m-30) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 1.4166 time to fit residues: 116.2294 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.049899 restraints weight = 27387.287| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.30 r_work: 0.2726 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.212 Angle : 0.559 7.019 11810 Z= 0.284 Chirality : 0.041 0.169 1376 Planarity : 0.005 0.046 1440 Dihedral : 7.992 123.393 1226 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.21 % Allowed : 7.49 % Favored : 91.30 % 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 (0.25), residues: 1070 helix: 1.49 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.003 0.001 HIS A 335 PHE 0.024 0.001 PHE A 251 TYR 0.027 0.001 TYR A 282 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.9323 (t70) cc_final: 0.8920 (p0) REVERT: A 349 MET cc_start: 0.9331 (mmm) cc_final: 0.8991 (mmm) REVERT: B 267 ASP cc_start: 0.8192 (t0) cc_final: 0.7889 (t0) REVERT: B 363 ASP cc_start: 0.9143 (m-30) cc_final: 0.8941 (m-30) outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 1.3576 time to fit residues: 109.9057 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 372 ASN B 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051233 restraints weight = 27137.405| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.30 r_work: 0.2766 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8688 Z= 0.152 Angle : 0.534 8.365 11810 Z= 0.271 Chirality : 0.039 0.158 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.627 123.272 1226 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.99 % Allowed : 9.80 % Favored : 89.21 % 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: 1.41 (0.25), residues: 1070 helix: 1.54 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.020 0.001 PHE A 251 TYR 0.026 0.001 TYR A 282 ARG 0.004 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.888 Fit side-chains REVERT: A 323 ASP cc_start: 0.9304 (t70) cc_final: 0.8903 (p0) REVERT: A 349 MET cc_start: 0.9360 (mmm) cc_final: 0.8976 (mmm) REVERT: B 267 ASP cc_start: 0.8153 (t0) cc_final: 0.7833 (t0) outliers start: 9 outliers final: 1 residues processed: 77 average time/residue: 1.3292 time to fit residues: 109.2673 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051144 restraints weight = 26975.365| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.29 r_work: 0.2758 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8688 Z= 0.173 Angle : 0.528 8.543 11810 Z= 0.270 Chirality : 0.040 0.165 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.568 119.864 1226 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.10 % Allowed : 10.24 % Favored : 88.66 % 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: 1.48 (0.25), residues: 1070 helix: 1.59 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.019 0.001 PHE B 251 TYR 0.025 0.001 TYR A 282 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.885 Fit side-chains REVERT: A 323 ASP cc_start: 0.9281 (t70) cc_final: 0.8921 (p0) REVERT: A 349 MET cc_start: 0.9359 (mmm) cc_final: 0.8948 (mmm) REVERT: B 267 ASP cc_start: 0.8190 (t0) cc_final: 0.7886 (t0) outliers start: 10 outliers final: 4 residues processed: 79 average time/residue: 1.2802 time to fit residues: 108.1298 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.067069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051872 restraints weight = 26766.802| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.30 r_work: 0.2778 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8688 Z= 0.154 Angle : 0.525 8.828 11810 Z= 0.267 Chirality : 0.039 0.155 1376 Planarity : 0.005 0.046 1440 Dihedral : 7.397 114.552 1226 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.88 % Allowed : 11.34 % Favored : 87.78 % 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: 1.51 (0.25), residues: 1070 helix: 1.62 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.017 0.001 PHE B 268 TYR 0.025 0.001 TYR A 282 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.953 Fit side-chains REVERT: A 349 MET cc_start: 0.9393 (mmm) cc_final: 0.8970 (mmm) REVERT: A 540 MET cc_start: 0.8731 (ttp) cc_final: 0.8355 (ttm) REVERT: B 110 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 267 ASP cc_start: 0.8246 (t0) cc_final: 0.7964 (t0) outliers start: 8 outliers final: 5 residues processed: 78 average time/residue: 1.2489 time to fit residues: 104.6095 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.067663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052323 restraints weight = 26730.503| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.32 r_work: 0.2779 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.155 Angle : 0.514 7.399 11810 Z= 0.264 Chirality : 0.039 0.158 1376 Planarity : 0.005 0.046 1440 Dihedral : 7.286 110.267 1226 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.99 % Allowed : 11.67 % Favored : 87.33 % 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: 1.53 (0.25), residues: 1070 helix: 1.64 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS B 335 PHE 0.018 0.001 PHE B 268 TYR 0.024 0.001 TYR A 282 ARG 0.007 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.010 Fit side-chains REVERT: A 349 MET cc_start: 0.9393 (mmm) cc_final: 0.8780 (mmm) REVERT: A 540 MET cc_start: 0.8725 (ttp) cc_final: 0.8353 (ttm) REVERT: B 110 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 118 MET cc_start: 0.8852 (ttm) cc_final: 0.8638 (ttm) REVERT: B 267 ASP cc_start: 0.8316 (t0) cc_final: 0.8063 (t0) REVERT: B 363 ASP cc_start: 0.8884 (m-30) cc_final: 0.8678 (m-30) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 1.3173 time to fit residues: 109.7965 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.067014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051723 restraints weight = 27054.657| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.34 r_work: 0.2773 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8688 Z= 0.172 Angle : 0.534 9.552 11810 Z= 0.269 Chirality : 0.039 0.161 1376 Planarity : 0.005 0.046 1440 Dihedral : 7.234 105.668 1226 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.10 % Allowed : 12.11 % Favored : 86.78 % 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: 1.58 (0.26), residues: 1070 helix: 1.72 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS B 335 PHE 0.015 0.001 PHE B 268 TYR 0.024 0.001 TYR A 282 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.825 Fit side-chains REVERT: A 349 MET cc_start: 0.9403 (mmm) cc_final: 0.8947 (mmm) REVERT: B 110 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8844 (mm) REVERT: B 118 MET cc_start: 0.8872 (ttm) cc_final: 0.8652 (ttm) REVERT: B 267 ASP cc_start: 0.8329 (t0) cc_final: 0.8067 (t0) REVERT: B 363 ASP cc_start: 0.8888 (m-30) cc_final: 0.8684 (m-30) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 1.2556 time to fit residues: 100.8514 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.066533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051023 restraints weight = 27049.530| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.35 r_work: 0.2753 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8688 Z= 0.195 Angle : 0.548 12.314 11810 Z= 0.274 Chirality : 0.040 0.164 1376 Planarity : 0.004 0.046 1440 Dihedral : 7.238 100.869 1226 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.99 % Allowed : 12.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1070 helix: 1.67 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS A 335 PHE 0.016 0.001 PHE A 251 TYR 0.023 0.001 TYR A 282 ARG 0.001 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.931 Fit side-chains REVERT: A 323 ASP cc_start: 0.9432 (t0) cc_final: 0.8905 (p0) REVERT: A 349 MET cc_start: 0.9398 (mmm) cc_final: 0.8951 (mmm) REVERT: B 110 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 267 ASP cc_start: 0.8351 (t0) cc_final: 0.8082 (t0) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 1.3017 time to fit residues: 101.4824 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050045 restraints weight = 27017.182| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.34 r_work: 0.2723 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8688 Z= 0.253 Angle : 0.586 14.536 11810 Z= 0.291 Chirality : 0.041 0.176 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.542 95.671 1226 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.99 % Allowed : 12.44 % Favored : 86.56 % 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: 1.53 (0.26), residues: 1070 helix: 1.62 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 414 HIS 0.004 0.001 HIS A 335 PHE 0.019 0.001 PHE A 251 TYR 0.022 0.001 TYR A 282 ARG 0.001 0.000 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.892 Fit side-chains REVERT: A 99 MET cc_start: 0.9550 (mtm) cc_final: 0.9316 (mtp) REVERT: A 241 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8414 (p) REVERT: A 323 ASP cc_start: 0.9439 (t0) cc_final: 0.8921 (p0) REVERT: A 349 MET cc_start: 0.9366 (mmm) cc_final: 0.8929 (mmm) REVERT: B 110 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 267 ASP cc_start: 0.8361 (t0) cc_final: 0.8113 (t0) REVERT: B 272 MET cc_start: 0.9452 (ttm) cc_final: 0.9207 (tpp) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 1.2325 time to fit residues: 99.0388 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.052108 restraints weight = 27137.202| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.36 r_work: 0.2779 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8688 Z= 0.146 Angle : 0.544 14.513 11810 Z= 0.272 Chirality : 0.039 0.151 1376 Planarity : 0.005 0.046 1440 Dihedral : 7.204 80.724 1226 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.99 % Allowed : 12.00 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1070 helix: 1.68 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.013 0.001 PHE B 251 TYR 0.024 0.001 TYR A 282 ARG 0.002 0.000 ARG B 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4441.65 seconds wall clock time: 79 minutes 32.50 seconds (4772.50 seconds total)