Starting phenix.real_space_refine on Thu Mar 6 05:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhs_38354/03_2025/8xhs_38354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhs_38354/03_2025/8xhs_38354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhs_38354/03_2025/8xhs_38354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhs_38354/03_2025/8xhs_38354.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhs_38354/03_2025/8xhs_38354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhs_38354/03_2025/8xhs_38354.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.072 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 26 5.16 5 C 3244 2.51 5 N 887 2.21 5 O 910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5067 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5044 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 597} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Time building chain proxies: 3.71, per 1000 atoms: 0.73 Number of scatterers: 5067 At special positions: 0 Unit cell: (73.186, 83.398, 108.928, 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 26 16.00 O 910 8.00 N 887 7.00 C 3244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 603.0 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 7 sheets defined 36.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.713A pdb=" N ALA A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.643A pdb=" N LEU A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.879A pdb=" N TYR A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.538A pdb=" N LYS A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 377 removed outlier: 4.170A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.518A pdb=" N ASN A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.503A pdb=" N SER A 449 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 450 " --> pdb=" O ILE A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 476 through 489 removed outlier: 4.223A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 4.438A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 614 removed outlier: 3.663A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.551A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.640A pdb=" N ALA A 631 " --> pdb=" O TYR A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.257A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 122 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 131 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN A 120 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 133 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 118 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU A 135 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LEU A 116 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.537A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.418A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 529 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 537 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY A 538 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET A 540 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 552 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 542 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 343 removed outlier: 6.619A pdb=" N GLY A 339 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR A 381 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 341 " --> pdb=" O THR A 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.372A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 214 hydrogen bonds defined for protein. 591 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: 1.42 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1627 1.34 - 1.46: 1067 1.46 - 1.58: 2425 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 5164 Sorted by residual: bond pdb=" CA GLU A 141 " pdb=" CB GLU A 141 " ideal model delta sigma weight residual 1.527 1.547 -0.019 1.70e-02 3.46e+03 1.31e+00 bond pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CA HIS A 696 " pdb=" C HIS A 696 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.12e-02 7.97e+03 9.44e-01 bond pdb=" CA GLU A 403 " pdb=" C GLU A 403 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.41e-02 5.03e+03 8.75e-01 bond pdb=" N LEU A 408 " pdb=" CA LEU A 408 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.93e-01 ... (remaining 5159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6810 1.39 - 2.78: 141 2.78 - 4.17: 23 4.17 - 5.56: 4 5.56 - 6.95: 3 Bond angle restraints: 6981 Sorted by residual: angle pdb=" CA GLU A 141 " pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA GLU A 403 " pdb=" C GLU A 403 " pdb=" N GLU A 404 " ideal model delta sigma weight residual 118.44 122.90 -4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C LEU A 408 " pdb=" CA LEU A 408 " pdb=" CB LEU A 408 " ideal model delta sigma weight residual 110.42 115.96 -5.54 1.99e+00 2.53e-01 7.75e+00 angle pdb=" N HIS A 320 " pdb=" CA HIS A 320 " pdb=" C HIS A 320 " ideal model delta sigma weight residual 114.09 110.47 3.62 1.55e+00 4.16e-01 5.47e+00 angle pdb=" C ALA A 46 " pdb=" N ASN A 47 " pdb=" CA ASN A 47 " ideal model delta sigma weight residual 121.54 125.44 -3.90 1.91e+00 2.74e-01 4.16e+00 ... (remaining 6976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 2705 16.62 - 33.23: 290 33.23 - 49.85: 63 49.85 - 66.46: 10 66.46 - 83.08: 3 Dihedral angle restraints: 3071 sinusoidal: 1247 harmonic: 1824 Sorted by residual: dihedral pdb=" CA PHE A 319 " pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLN A 284 " pdb=" C GLN A 284 " pdb=" N GLN A 285 " pdb=" CA GLN A 285 " ideal model delta harmonic sigma weight residual 180.00 164.77 15.23 0 5.00e+00 4.00e-02 9.28e+00 ... (remaining 3068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 491 0.032 - 0.063: 187 0.063 - 0.095: 55 0.095 - 0.127: 38 0.127 - 0.158: 3 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA ILE A 671 " pdb=" N ILE A 671 " pdb=" C ILE A 671 " pdb=" CB ILE A 671 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA GLU A 141 " pdb=" N GLU A 141 " pdb=" C GLU A 141 " pdb=" CB GLU A 141 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 771 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 682 " 0.010 2.00e-02 2.50e+03 1.07e-02 2.00e+00 pdb=" CG PHE A 682 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 682 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 682 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 682 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 682 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 682 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO A 511 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 680 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 681 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.018 5.00e-02 4.00e+02 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 453 2.75 - 3.29: 4697 3.29 - 3.82: 7870 3.82 - 4.36: 9631 4.36 - 4.90: 17008 Nonbonded interactions: 39659 Sorted by model distance: nonbonded pdb=" OG1 THR A 402 " pdb=" OE1 GLU A 404 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 668 " pdb=" O HOH A 801 " model vdw 2.278 3.040 nonbonded pdb=" N GLY A 645 " pdb=" O CYS A 657 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS A 334 " pdb=" O ALA A 375 " model vdw 2.325 3.120 nonbonded pdb=" OG SER A 423 " pdb=" OE2 GLU A 454 " model vdw 2.328 3.040 ... (remaining 39654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.002 0.032 5164 Z= 0.158 Angle : 0.510 6.948 6981 Z= 0.281 Chirality : 0.042 0.158 774 Planarity : 0.003 0.034 882 Dihedral : 14.235 83.079 1891 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.16 (0.34), residues: 608 helix: 1.22 (0.38), residues: 201 sheet: 0.67 (0.48), residues: 120 loop : -0.96 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.002 0.000 HIS A 696 PHE 0.024 0.001 PHE A 682 TYR 0.009 0.001 TYR A 53 ARG 0.002 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.572 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.6748 (tt0) cc_final: 0.6534 (tt0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 1.2938 time to fit residues: 117.0419 Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 25 optimal weight: 0.0670 chunk 15 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 120 GLN A 289 GLN A 439 GLN A 461 GLN A 546 GLN A 674 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159218 restraints weight = 5362.682| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.51 r_work: 0.3496 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5164 Z= 0.119 Angle : 0.459 5.763 6981 Z= 0.246 Chirality : 0.041 0.152 774 Planarity : 0.003 0.039 882 Dihedral : 3.961 19.490 673 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.92 % Allowed : 11.58 % Favored : 87.50 % 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: 0.46 (0.34), residues: 608 helix: 1.47 (0.38), residues: 209 sheet: 0.83 (0.49), residues: 120 loop : -0.82 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.014 0.001 PHE A 682 TYR 0.006 0.001 TYR A 53 ARG 0.003 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.643 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.6779 (tt0) cc_final: 0.6479 (tt0) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 1.4268 time to fit residues: 107.6317 Evaluate side-chains 60 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 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 = 0.4258 r_free = 0.4258 target = 0.199336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156332 restraints weight = 5390.795| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.44 r_work: 0.3431 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5164 Z= 0.167 Angle : 0.477 4.961 6981 Z= 0.258 Chirality : 0.042 0.149 774 Planarity : 0.003 0.043 882 Dihedral : 4.072 19.736 673 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.29 % Allowed : 14.52 % Favored : 84.19 % 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: 0.54 (0.35), residues: 608 helix: 1.57 (0.38), residues: 209 sheet: 0.77 (0.47), residues: 132 loop : -0.83 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.013 0.001 PHE A 682 TYR 0.008 0.001 TYR A 158 ARG 0.007 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.522 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7014 (tt0) cc_final: 0.6690 (tt0) outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 1.4912 time to fit residues: 104.0663 Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.195715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152872 restraints weight = 5396.710| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.61 r_work: 0.3390 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5164 Z= 0.223 Angle : 0.512 5.341 6981 Z= 0.277 Chirality : 0.043 0.157 774 Planarity : 0.003 0.046 882 Dihedral : 4.382 20.885 673 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.39 % Allowed : 15.62 % Favored : 81.99 % 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: 0.37 (0.34), residues: 608 helix: 1.44 (0.38), residues: 209 sheet: 0.95 (0.50), residues: 113 loop : -0.97 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.012 0.001 PHE A 420 TYR 0.011 0.001 TYR A 158 ARG 0.007 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.646 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7189 (tt0) cc_final: 0.6775 (tt0) REVERT: A 548 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7379 (p90) REVERT: A 700 MET cc_start: 0.8891 (tpt) cc_final: 0.8622 (tpt) outliers start: 13 outliers final: 5 residues processed: 69 average time/residue: 1.9809 time to fit residues: 142.8239 Evaluate side-chains 66 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.0070 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.196724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154309 restraints weight = 5347.409| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.41 r_work: 0.3429 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5164 Z= 0.179 Angle : 0.482 5.380 6981 Z= 0.261 Chirality : 0.042 0.154 774 Planarity : 0.003 0.046 882 Dihedral : 4.274 20.867 673 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.84 % Allowed : 17.83 % Favored : 80.33 % 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: 0.41 (0.34), residues: 608 helix: 1.52 (0.38), residues: 209 sheet: 0.85 (0.48), residues: 120 loop : -0.97 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.002 0.001 HIS A 467 PHE 0.009 0.001 PHE A 420 TYR 0.009 0.001 TYR A 158 ARG 0.008 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.713 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 13 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7371 (mmm160) REVERT: A 531 GLU cc_start: 0.7167 (tt0) cc_final: 0.6790 (tt0) REVERT: A 548 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7333 (p90) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 1.2318 time to fit residues: 84.1437 Evaluate side-chains 64 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138323 restraints weight = 5375.635| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.08 r_work: 0.3405 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5164 Z= 0.286 Angle : 0.547 5.632 6981 Z= 0.296 Chirality : 0.044 0.163 774 Planarity : 0.004 0.047 882 Dihedral : 4.566 22.131 673 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.39 % Allowed : 18.01 % Favored : 79.60 % 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: 0.13 (0.33), residues: 608 helix: 1.29 (0.37), residues: 209 sheet: 1.14 (0.52), residues: 98 loop : -1.19 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 512 HIS 0.003 0.001 HIS A 548 PHE 0.013 0.002 PHE A 420 TYR 0.013 0.001 TYR A 158 ARG 0.008 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.566 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7345 (tt0) cc_final: 0.6827 (tt0) REVERT: A 548 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7425 (p90) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 1.3378 time to fit residues: 95.2029 Evaluate side-chains 68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.195473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148959 restraints weight = 5339.689| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.14 r_work: 0.3406 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5164 Z= 0.177 Angle : 0.489 5.942 6981 Z= 0.265 Chirality : 0.042 0.154 774 Planarity : 0.003 0.046 882 Dihedral : 4.328 21.369 673 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.84 % Allowed : 19.67 % Favored : 78.49 % 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: 0.33 (0.34), residues: 608 helix: 1.44 (0.38), residues: 209 sheet: 1.05 (0.50), residues: 114 loop : -1.10 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.008 0.001 PHE A 420 TYR 0.011 0.001 TYR A 37 ARG 0.010 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.531 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7240 (tt0) cc_final: 0.6726 (tt0) REVERT: A 548 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7372 (p90) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 1.2495 time to fit residues: 86.3278 Evaluate side-chains 67 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.195207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139842 restraints weight = 5355.464| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.09 r_work: 0.3438 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5164 Z= 0.201 Angle : 0.503 6.114 6981 Z= 0.272 Chirality : 0.043 0.156 774 Planarity : 0.004 0.046 882 Dihedral : 4.321 21.200 673 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.02 % Allowed : 19.67 % Favored : 78.31 % 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: 0.26 (0.33), residues: 608 helix: 1.40 (0.37), residues: 209 sheet: 1.28 (0.53), residues: 98 loop : -1.15 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.010 0.001 PHE A 420 TYR 0.010 0.001 TYR A 158 ARG 0.010 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.607 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7354 (tt0) cc_final: 0.6820 (tt0) REVERT: A 548 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7447 (p90) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 1.5013 time to fit residues: 104.5462 Evaluate side-chains 68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.195170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153011 restraints weight = 5274.535| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.49 r_work: 0.3414 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5164 Z= 0.169 Angle : 0.488 6.483 6981 Z= 0.264 Chirality : 0.042 0.151 774 Planarity : 0.003 0.046 882 Dihedral : 4.228 20.921 673 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.65 % Allowed : 20.22 % Favored : 78.12 % 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: 0.38 (0.34), residues: 608 helix: 1.48 (0.38), residues: 209 sheet: 1.02 (0.49), residues: 120 loop : -1.07 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.008 0.001 PHE A 420 TYR 0.018 0.001 TYR A 37 ARG 0.011 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.589 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7257 (tt0) cc_final: 0.6754 (tt0) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 1.4861 time to fit residues: 101.5678 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.196243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143211 restraints weight = 5328.415| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.22 r_work: 0.3461 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5164 Z= 0.178 Angle : 0.503 6.781 6981 Z= 0.271 Chirality : 0.042 0.152 774 Planarity : 0.004 0.047 882 Dihedral : 4.214 20.887 673 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.65 % Allowed : 19.85 % Favored : 78.49 % 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: 0.33 (0.34), residues: 608 helix: 1.48 (0.38), residues: 209 sheet: 1.18 (0.52), residues: 104 loop : -1.10 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.009 0.001 PHE A 420 TYR 0.009 0.001 TYR A 53 ARG 0.011 0.000 ARG A 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.606 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7334 (tt0) cc_final: 0.6803 (tt0) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 1.0827 time to fit residues: 71.9226 Evaluate side-chains 64 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.195968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140347 restraints weight = 5414.673| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.12 r_work: 0.3447 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5164 Z= 0.196 Angle : 0.522 8.301 6981 Z= 0.280 Chirality : 0.043 0.156 774 Planarity : 0.004 0.053 882 Dihedral : 4.276 20.809 673 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.47 % Allowed : 20.04 % Favored : 78.49 % 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: 0.30 (0.34), residues: 608 helix: 1.41 (0.37), residues: 209 sheet: 1.21 (0.52), residues: 104 loop : -1.12 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.009 0.001 PHE A 420 TYR 0.022 0.001 TYR A 37 ARG 0.013 0.000 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5030.00 seconds wall clock time: 92 minutes 11.18 seconds (5531.18 seconds total)