Starting phenix.real_space_refine on Tue Feb 11 00:39:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wr8_32718/02_2025/7wr8_32718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr8_32718/02_2025/7wr8_32718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wr8_32718/02_2025/7wr8_32718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr8_32718/02_2025/7wr8_32718.map" model { file = "/net/cci-nas-00/data/ceres_data/7wr8_32718/02_2025/7wr8_32718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr8_32718/02_2025/7wr8_32718.cif" } resolution = 3.5 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= 0.000 sd= 0.026 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 15 5.16 5 C 2086 2.51 5 N 555 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3286 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.28, per 1000 atoms: 1.00 Number of scatterers: 3286 At special positions: 0 Unit cell: (100.88, 62.4, 69.68, 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 15 16.00 O 630 8.00 N 555 7.00 C 2086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 353.9 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 9.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.925A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.319A pdb=" N VAL R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.912A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.804A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.668A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.631A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.353A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.522A pdb=" N SER A 17 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 83 " --> pdb=" O SER A 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.146A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.857A pdb=" N THR B 73 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.891A pdb=" N THR B 103 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 45 " --> pdb=" O GLN B 36 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 174 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: 0.83 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 813 1.33 - 1.45: 759 1.45 - 1.57: 1783 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3373 Sorted by residual: bond pdb=" CG LEU R 441 " pdb=" CD2 LEU R 441 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" C GLU B 52 " pdb=" N ARG B 53 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.05e-02 9.07e+03 4.83e+00 bond pdb=" C ASP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" C SER B 13 " pdb=" N PRO B 14 " ideal model delta sigma weight residual 1.332 1.357 -0.026 1.34e-02 5.57e+03 3.63e+00 bond pdb=" CB TRP A 47 " pdb=" CG TRP A 47 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 4546 4.43 - 8.86: 45 8.86 - 13.29: 1 13.29 - 17.72: 0 17.72 - 22.15: 1 Bond angle restraints: 4593 Sorted by residual: angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 138.45 -22.15 3.50e+00 8.16e-02 4.00e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " ideal model delta sigma weight residual 116.20 120.25 -4.05 8.00e-01 1.56e+00 2.57e+01 angle pdb=" N ASN R 477 " pdb=" CA ASN R 477 " pdb=" C ASN R 477 " ideal model delta sigma weight residual 110.97 116.45 -5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 121.31 118.05 3.26 7.40e-01 1.83e+00 1.94e+01 angle pdb=" C LYS B 49 " pdb=" N ASP B 50 " pdb=" CA ASP B 50 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1763 15.93 - 31.86: 206 31.86 - 47.79: 45 47.79 - 63.72: 2 63.72 - 79.64: 4 Dihedral angle restraints: 2020 sinusoidal: 818 harmonic: 1202 Sorted by residual: dihedral pdb=" CA SER B 93 " pdb=" C SER B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " pdb=" CB CYS B 87 " ideal model delta sinusoidal sigma weight residual 93.00 47.57 45.43 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 2017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 342 0.052 - 0.105: 108 0.105 - 0.157: 42 0.157 - 0.210: 6 0.210 - 0.262: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.18e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" CB ILE A 19 " pdb=" CA ILE A 19 " pdb=" CG1 ILE A 19 " pdb=" CG2 ILE A 19 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.136 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG C 1 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 118 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 118 " -0.026 2.00e-02 2.50e+03 pdb=" N TRP A 119 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 27 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO B 28 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 597 2.76 - 3.30: 2775 3.30 - 3.83: 5395 3.83 - 4.37: 6177 4.37 - 4.90: 11042 Nonbonded interactions: 25986 Sorted by model distance: nonbonded pdb=" NZ LYS R 440 " pdb=" N SER A 104 " model vdw 2.230 3.200 nonbonded pdb=" OG SER R 359 " pdb=" OD1 ASN R 394 " model vdw 2.295 3.040 nonbonded pdb=" O SER B 29 " pdb=" OG SER B 29 " model vdw 2.302 3.040 nonbonded pdb=" NE2 HIS A 35 " pdb=" OD1 ASP A 99 " model vdw 2.307 3.120 nonbonded pdb=" OH TYR B 35 " pdb=" OE1 GLN B 88 " model vdw 2.328 3.040 ... (remaining 25981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.008 0.084 3373 Z= 0.558 Angle : 1.160 22.149 4593 Z= 0.630 Chirality : 0.062 0.262 502 Planarity : 0.010 0.111 591 Dihedral : 13.718 79.644 1245 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.38), residues: 409 helix: -3.53 (0.89), residues: 21 sheet: -1.93 (0.42), residues: 139 loop : -2.50 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 47 HIS 0.004 0.001 HIS A 32 PHE 0.050 0.004 PHE R 456 TYR 0.035 0.003 TYR R 501 ARG 0.015 0.002 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.367 Fit side-chains REVERT: A 80 TYR cc_start: 0.7233 (m-80) cc_final: 0.7012 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1525 time to fit residues: 13.7461 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 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 = 0.3892 r_free = 0.3892 target = 0.173942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145208 restraints weight = 3687.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148927 restraints weight = 2585.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151547 restraints weight = 2031.330| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3373 Z= 0.263 Angle : 0.696 10.891 4593 Z= 0.358 Chirality : 0.046 0.138 502 Planarity : 0.006 0.064 591 Dihedral : 6.695 27.476 524 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 1.42 % Allowed : 9.66 % Favored : 88.92 % 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: -3.20 (0.39), residues: 409 helix: -3.77 (0.71), residues: 27 sheet: -1.69 (0.42), residues: 144 loop : -2.24 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 119 HIS 0.001 0.001 HIS B 97 PHE 0.015 0.001 PHE A 101 TYR 0.018 0.001 TYR R 495 ARG 0.005 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.342 Fit side-chains REVERT: A 87 ARG cc_start: 0.6894 (mtm-85) cc_final: 0.6581 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.1688 time to fit residues: 15.1962 Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.174942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.147320 restraints weight = 3611.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.151029 restraints weight = 2509.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153692 restraints weight = 1941.907| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3373 Z= 0.232 Angle : 0.644 8.586 4593 Z= 0.331 Chirality : 0.045 0.141 502 Planarity : 0.005 0.058 591 Dihedral : 6.133 26.910 524 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 1.42 % Allowed : 11.65 % Favored : 86.93 % 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: -2.99 (0.40), residues: 409 helix: -3.90 (0.79), residues: 20 sheet: -1.63 (0.42), residues: 142 loop : -2.07 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 119 HIS 0.001 0.000 HIS R 505 PHE 0.012 0.001 PHE A 101 TYR 0.017 0.001 TYR R 495 ARG 0.007 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.328 Fit side-chains REVERT: R 396 TYR cc_start: 0.7791 (m-80) cc_final: 0.7524 (m-80) REVERT: B 91 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6700 (t0) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.1586 time to fit residues: 13.7716 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 29 optimal weight: 0.0670 chunk 32 optimal weight: 0.0060 overall best weight: 0.4534 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.165288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134387 restraints weight = 3878.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138266 restraints weight = 2644.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141060 restraints weight = 2054.059| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3373 Z= 0.191 Angle : 0.596 6.938 4593 Z= 0.305 Chirality : 0.044 0.135 502 Planarity : 0.005 0.049 591 Dihedral : 5.606 25.214 524 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.56 % Allowed : 11.65 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.41), residues: 409 helix: -3.92 (0.73), residues: 20 sheet: -1.53 (0.43), residues: 141 loop : -1.93 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 119 HIS 0.001 0.000 HIS A 35 PHE 0.019 0.001 PHE R 456 TYR 0.014 0.001 TYR R 495 ARG 0.005 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.374 Fit side-chains REVERT: R 396 TYR cc_start: 0.7812 (m-80) cc_final: 0.7578 (m-80) REVERT: A 80 TYR cc_start: 0.7042 (m-10) cc_final: 0.6640 (m-80) REVERT: A 103 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4774 (pp) REVERT: B 91 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6673 (t0) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1505 time to fit residues: 12.2707 Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.175438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150692 restraints weight = 3714.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151154 restraints weight = 2861.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152207 restraints weight = 2653.162| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3373 Z= 0.219 Angle : 0.611 8.751 4593 Z= 0.310 Chirality : 0.044 0.133 502 Planarity : 0.005 0.050 591 Dihedral : 5.555 26.515 524 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 1.70 % Allowed : 14.77 % Favored : 83.52 % 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: -2.74 (0.41), residues: 409 helix: -3.95 (0.69), residues: 20 sheet: -1.49 (0.43), residues: 141 loop : -1.86 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 PHE 0.015 0.001 PHE R 456 TYR 0.015 0.001 TYR R 495 ARG 0.004 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.381 Fit side-chains REVERT: R 396 TYR cc_start: 0.7775 (m-80) cc_final: 0.7541 (m-80) REVERT: A 80 TYR cc_start: 0.6993 (m-10) cc_final: 0.6705 (m-80) REVERT: A 103 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4830 (pp) REVERT: A 109 TRP cc_start: 0.8991 (m-10) cc_final: 0.8430 (m-10) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.1632 time to fit residues: 13.4517 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.175825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.149835 restraints weight = 3783.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.149658 restraints weight = 3072.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150797 restraints weight = 2744.462| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3373 Z= 0.214 Angle : 0.600 7.749 4593 Z= 0.304 Chirality : 0.044 0.132 502 Planarity : 0.005 0.045 591 Dihedral : 5.399 25.829 524 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.56 % Allowed : 15.91 % Favored : 81.53 % 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: -2.69 (0.41), residues: 409 helix: -3.96 (0.68), residues: 20 sheet: -1.43 (0.44), residues: 141 loop : -1.84 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 PHE 0.018 0.001 PHE R 456 TYR 0.015 0.001 TYR R 495 ARG 0.006 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.361 Fit side-chains REVERT: R 396 TYR cc_start: 0.7806 (m-80) cc_final: 0.7560 (m-80) REVERT: A 103 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4795 (pp) REVERT: B 91 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6678 (t0) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1510 time to fit residues: 13.6190 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.162035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135361 restraints weight = 3861.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135613 restraints weight = 3151.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137063 restraints weight = 3139.028| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3373 Z= 0.266 Angle : 0.627 7.317 4593 Z= 0.320 Chirality : 0.045 0.130 502 Planarity : 0.005 0.047 591 Dihedral : 5.486 26.450 524 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.41 % Allowed : 16.19 % Favored : 80.40 % 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: -2.65 (0.41), residues: 409 helix: -3.66 (0.91), residues: 14 sheet: -1.32 (0.44), residues: 135 loop : -1.96 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.002 0.001 HIS R 505 PHE 0.018 0.001 PHE R 456 TYR 0.016 0.001 TYR R 495 ARG 0.005 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.367 Fit side-chains REVERT: R 374 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5325 (t80) REVERT: R 396 TYR cc_start: 0.7771 (m-80) cc_final: 0.7534 (m-80) REVERT: A 103 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4916 (pp) REVERT: A 109 TRP cc_start: 0.9023 (m-10) cc_final: 0.8468 (m-10) REVERT: B 91 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6607 (t0) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.1327 time to fit residues: 12.2331 Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 3 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 = 0.3787 r_free = 0.3787 target = 0.162757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136797 restraints weight = 3868.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137732 restraints weight = 3066.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139300 restraints weight = 2774.201| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3373 Z= 0.238 Angle : 0.629 11.055 4593 Z= 0.316 Chirality : 0.045 0.128 502 Planarity : 0.005 0.045 591 Dihedral : 5.417 26.350 524 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 3.41 % Allowed : 16.76 % Favored : 79.83 % 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: -2.66 (0.41), residues: 409 helix: -3.59 (0.93), residues: 14 sheet: -1.41 (0.44), residues: 141 loop : -1.92 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.002 0.001 HIS A 35 PHE 0.022 0.001 PHE R 456 TYR 0.014 0.001 TYR R 495 ARG 0.007 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.336 Fit side-chains REVERT: R 396 TYR cc_start: 0.7790 (m-80) cc_final: 0.7543 (m-80) REVERT: A 103 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4841 (pp) REVERT: B 91 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6625 (t0) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.1447 time to fit residues: 12.9253 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.163712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133171 restraints weight = 3859.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136629 restraints weight = 2816.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139045 restraints weight = 2262.975| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3373 Z= 0.290 Angle : 0.672 10.426 4593 Z= 0.341 Chirality : 0.047 0.261 502 Planarity : 0.005 0.046 591 Dihedral : 5.525 26.742 524 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 3.41 % Allowed : 17.05 % Favored : 79.55 % 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: -2.64 (0.41), residues: 409 helix: -3.60 (0.94), residues: 14 sheet: -1.30 (0.45), residues: 135 loop : -1.97 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 PHE 0.022 0.002 PHE R 456 TYR 0.014 0.001 TYR R 495 ARG 0.006 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.456 Fit side-chains REVERT: R 396 TYR cc_start: 0.7814 (m-80) cc_final: 0.7572 (m-80) REVERT: A 103 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4974 (pp) REVERT: B 91 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6742 (t0) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1533 time to fit residues: 14.0584 Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.166041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135144 restraints weight = 3769.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138979 restraints weight = 2635.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141487 restraints weight = 2068.265| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3373 Z= 0.228 Angle : 0.637 9.914 4593 Z= 0.325 Chirality : 0.046 0.229 502 Planarity : 0.005 0.048 591 Dihedral : 5.417 26.057 524 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.84 % Allowed : 17.61 % Favored : 79.55 % 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: -2.53 (0.41), residues: 409 helix: -3.52 (0.95), residues: 14 sheet: -1.05 (0.46), residues: 130 loop : -1.99 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 119 HIS 0.001 0.001 HIS A 35 PHE 0.025 0.002 PHE R 456 TYR 0.013 0.001 TYR R 495 ARG 0.006 0.001 ARG A 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.341 Fit side-chains REVERT: R 396 TYR cc_start: 0.7751 (m-80) cc_final: 0.7524 (m-80) REVERT: A 103 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4841 (pp) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.1490 time to fit residues: 13.2497 Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.163358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132772 restraints weight = 3873.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136024 restraints weight = 2845.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138462 restraints weight = 2300.183| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3373 Z= 0.286 Angle : 0.664 10.290 4593 Z= 0.338 Chirality : 0.046 0.210 502 Planarity : 0.005 0.042 591 Dihedral : 5.555 27.019 524 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.56 % Allowed : 18.18 % Favored : 79.26 % 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: -2.64 (0.41), residues: 409 helix: -3.60 (0.92), residues: 14 sheet: -1.09 (0.46), residues: 132 loop : -2.09 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.001 0.001 HIS R 505 PHE 0.023 0.002 PHE R 456 TYR 0.015 0.001 TYR R 495 ARG 0.008 0.001 ARG A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.96 seconds wall clock time: 29 minutes 2.49 seconds (1742.49 seconds total)