Starting phenix.real_space_refine on Tue Jan 14 03:13:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsi_38619/01_2025/8xsi_38619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsi_38619/01_2025/8xsi_38619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsi_38619/01_2025/8xsi_38619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsi_38619/01_2025/8xsi_38619.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsi_38619/01_2025/8xsi_38619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsi_38619/01_2025/8xsi_38619.cif" } resolution = 2.1 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2404 atoms to isotropic. 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 17 5.16 5 C 2124 2.51 5 N 565 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3354 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} bond proxies already assigned to first conformer: 1580 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 975 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.72, per 1000 atoms: 1.11 Number of scatterers: 3354 At special positions: 0 Unit cell: (62.9, 76.5, 89.25, 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 17 16.00 O 648 8.00 N 565 7.00 C 2124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 109 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 548.9 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 10.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.326A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.522A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.549A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.853A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.566A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 255 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: 0.89 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1072 1.35 - 1.48: 973 1.48 - 1.60: 1374 1.60 - 1.72: 0 1.72 - 1.85: 20 Bond restraints: 3439 Sorted by residual: bond pdb=" CB CYS H 109 " pdb=" SG CYS H 109 " ideal model delta sigma weight residual 1.808 1.849 -0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3 NAG B 601 " pdb=" O3 NAG B 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CG PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.67e-01 ... (remaining 3434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 4442 1.23 - 2.45: 176 2.45 - 3.68: 42 3.68 - 4.91: 8 4.91 - 6.13: 2 Bond angle restraints: 4670 Sorted by residual: angle pdb=" C SER H 108 " pdb=" N CYS H 109 " pdb=" CA CYS H 109 " ideal model delta sigma weight residual 122.08 125.77 -3.69 1.47e+00 4.63e-01 6.31e+00 angle pdb=" C ALA L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.05e+00 angle pdb=" C SER L 14 " pdb=" N VAL L 15 " pdb=" CA VAL L 15 " ideal model delta sigma weight residual 120.63 123.54 -2.91 1.33e+00 5.65e-01 4.78e+00 angle pdb=" C LYS H 58 " pdb=" N TYR H 59 " pdb=" CA TYR H 59 " ideal model delta sigma weight residual 122.29 118.73 3.56 1.65e+00 3.67e-01 4.66e+00 angle pdb=" C VAL B 362 " pdb=" N ALA B 363 " pdb=" CA ALA B 363 " ideal model delta sigma weight residual 121.56 124.63 -3.07 1.56e+00 4.11e-01 3.87e+00 ... (remaining 4665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 1831 14.10 - 28.21: 150 28.21 - 42.31: 41 42.31 - 56.41: 9 56.41 - 70.52: 6 Dihedral angle restraints: 2037 sinusoidal: 798 harmonic: 1239 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.93 56.07 1 1.00e+01 1.00e-02 4.24e+01 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASN H 74 " pdb=" C ASN H 74 " pdb=" N SER H 75 " pdb=" CA SER H 75 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 311 0.036 - 0.071: 129 0.071 - 0.107: 36 0.107 - 0.142: 20 0.142 - 0.178: 2 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA CYS H 109 " pdb=" N CYS H 109 " pdb=" C CYS H 109 " pdb=" CB CYS H 109 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA PRO L 44 " pdb=" N PRO L 44 " pdb=" C PRO L 44 " pdb=" CB PRO L 44 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA CYS H 104 " pdb=" N CYS H 104 " pdb=" C CYS H 104 " pdb=" CB CYS H 104 " 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 495 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO L 80 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 521 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO L 44 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.020 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 65 2.69 - 3.24: 2922 3.24 - 3.79: 4850 3.79 - 4.35: 6992 4.35 - 4.90: 11499 Nonbonded interactions: 26328 Sorted by model distance: nonbonded pdb=" OD1 ASN B 354 " pdb=" OG SER B 399 " model vdw 2.136 3.040 nonbonded pdb=" OD2 ASP H 54 " pdb=" OG SER H 56 " model vdw 2.165 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 2.272 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.278 3.040 ... (remaining 26323 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.740 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3439 Z= 0.198 Angle : 0.604 6.133 4670 Z= 0.327 Chirality : 0.046 0.178 498 Planarity : 0.004 0.055 604 Dihedral : 12.125 70.517 1239 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 0.55 % Allowed : 0.00 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.70 (0.40), residues: 424 helix: -3.12 (0.78), residues: 24 sheet: 0.52 (0.42), residues: 159 loop : -0.86 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 116 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE B 486 TYR 0.015 0.001 TYR B 495 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.408 Fit side-chains REVERT: B 370 ASN cc_start: 0.7194 (m-40) cc_final: 0.6819 (m-40) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.8053 time to fit residues: 47.2226 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN H 35 HIS H 77 ASN L 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.147275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129367 restraints weight = 9052.285| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.46 r_work: 0.3771 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3439 Z= 0.307 Angle : 0.647 5.909 4670 Z= 0.347 Chirality : 0.048 0.178 498 Planarity : 0.005 0.057 604 Dihedral : 6.036 57.816 500 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 2.47 % Allowed : 5.22 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.85 (0.40), residues: 424 helix: -3.32 (0.76), residues: 24 sheet: 0.44 (0.40), residues: 169 loop : -1.02 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 116 HIS 0.004 0.002 HIS H 35 PHE 0.014 0.002 PHE B 515 TYR 0.017 0.002 TYR B 495 ARG 0.004 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.332 Fit side-chains REVERT: B 356 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7913 (ttmm) REVERT: B 370 ASN cc_start: 0.7330 (m-40) cc_final: 0.6937 (m-40) REVERT: B 468 ILE cc_start: 0.8236 (pt) cc_final: 0.8004 (mm) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 0.8922 time to fit residues: 54.8881 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 17 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 506 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.149606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131870 restraints weight = 9358.895| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.50 r_work: 0.3810 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3439 Z= 0.145 Angle : 0.534 5.215 4670 Z= 0.285 Chirality : 0.044 0.140 498 Planarity : 0.004 0.054 604 Dihedral : 5.518 55.317 500 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.20 % Allowed : 7.14 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.86 (0.40), residues: 424 helix: -3.43 (0.65), residues: 32 sheet: 0.60 (0.40), residues: 166 loop : -1.03 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.009 0.001 TYR B 495 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.361 Fit side-chains REVERT: B 370 ASN cc_start: 0.7367 (m-40) cc_final: 0.7027 (m-40) REVERT: B 468 ILE cc_start: 0.8189 (pt) cc_final: 0.7965 (mm) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.8522 time to fit residues: 49.1951 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.0670 chunk 36 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.149193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.133012 restraints weight = 6198.225| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.94 r_work: 0.3844 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3439 Z= 0.173 Angle : 0.549 6.249 4670 Z= 0.293 Chirality : 0.044 0.149 498 Planarity : 0.004 0.052 604 Dihedral : 5.552 55.722 500 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.75 % Allowed : 8.24 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.84 (0.40), residues: 424 helix: -3.55 (0.62), residues: 32 sheet: 0.65 (0.40), residues: 166 loop : -1.03 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.355 Fit side-chains REVERT: B 370 ASN cc_start: 0.7328 (m-40) cc_final: 0.7024 (m-40) REVERT: B 468 ILE cc_start: 0.8157 (pt) cc_final: 0.7953 (mm) outliers start: 8 outliers final: 2 residues processed: 59 average time/residue: 0.7951 time to fit residues: 49.1749 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 17 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133565 restraints weight = 4338.208| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.57 r_work: 0.3859 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3439 Z= 0.209 Angle : 0.576 6.832 4670 Z= 0.306 Chirality : 0.045 0.156 498 Planarity : 0.004 0.052 604 Dihedral : 5.680 56.401 500 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.20 % Allowed : 9.34 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.76 (0.40), residues: 424 helix: -3.57 (0.70), residues: 24 sheet: 0.57 (0.40), residues: 168 loop : -0.97 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE B 515 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.362 Fit side-chains REVERT: B 370 ASN cc_start: 0.7311 (m-40) cc_final: 0.7011 (m-40) REVERT: B 468 ILE cc_start: 0.8145 (pt) cc_final: 0.7944 (mm) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.8838 time to fit residues: 52.6021 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 34 optimal weight: 0.0470 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.149445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130565 restraints weight = 12149.813| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.91 r_work: 0.3771 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3439 Z= 0.165 Angle : 0.543 7.197 4670 Z= 0.288 Chirality : 0.044 0.146 498 Planarity : 0.004 0.052 604 Dihedral : 5.529 55.525 500 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.20 % Allowed : 9.89 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.73 (0.40), residues: 424 helix: -3.55 (0.71), residues: 24 sheet: 0.58 (0.40), residues: 168 loop : -0.94 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE L 83 TYR 0.010 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.337 Fit side-chains REVERT: B 370 ASN cc_start: 0.7321 (m-40) cc_final: 0.7006 (m-40) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.8568 time to fit residues: 49.2712 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.132142 restraints weight = 6540.076| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.00 r_work: 0.3824 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3439 Z= 0.205 Angle : 0.576 7.984 4670 Z= 0.304 Chirality : 0.045 0.156 498 Planarity : 0.004 0.051 604 Dihedral : 5.658 56.370 500 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 3.02 % Allowed : 9.34 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.77 (0.40), residues: 424 helix: -3.56 (0.69), residues: 25 sheet: 0.56 (0.40), residues: 168 loop : -0.98 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE B 515 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.340 Fit side-chains REVERT: B 370 ASN cc_start: 0.7350 (m-40) cc_final: 0.7049 (m-40) REVERT: B 468 ILE cc_start: 0.8219 (pt) cc_final: 0.7994 (mm) outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.8816 time to fit residues: 52.4517 Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.0050 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.130288 restraints weight = 12514.122| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.97 r_work: 0.3767 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3439 Z= 0.171 Angle : 0.555 8.689 4670 Z= 0.292 Chirality : 0.045 0.146 498 Planarity : 0.004 0.051 604 Dihedral : 5.549 55.661 500 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.47 % Allowed : 10.44 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.75 (0.40), residues: 424 helix: -3.55 (0.68), residues: 25 sheet: 0.56 (0.40), residues: 168 loop : -0.94 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.357 Fit side-chains REVERT: B 370 ASN cc_start: 0.7345 (m-40) cc_final: 0.7028 (m-40) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.9111 time to fit residues: 52.2268 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 0.0670 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.150177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130436 restraints weight = 14828.124| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 3.27 r_work: 0.3761 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3439 Z= 0.152 Angle : 0.555 9.878 4670 Z= 0.289 Chirality : 0.044 0.137 498 Planarity : 0.004 0.051 604 Dihedral : 5.463 55.225 500 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.20 % Allowed : 11.26 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.73 (0.40), residues: 424 helix: -3.53 (0.69), residues: 25 sheet: 0.58 (0.40), residues: 168 loop : -0.94 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE L 83 TYR 0.009 0.001 TYR B 495 ARG 0.003 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.370 Fit side-chains REVERT: B 370 ASN cc_start: 0.7345 (m-40) cc_final: 0.7039 (m-40) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.8296 time to fit residues: 49.4489 Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.131426 restraints weight = 9335.049| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.48 r_work: 0.3802 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3439 Z= 0.180 Angle : 0.581 10.548 4670 Z= 0.304 Chirality : 0.045 0.147 498 Planarity : 0.004 0.050 604 Dihedral : 5.568 55.775 500 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 1.37 % Allowed : 12.64 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.72 (0.40), residues: 424 helix: -3.51 (0.70), residues: 25 sheet: 0.61 (0.40), residues: 168 loop : -0.96 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.376 Fit side-chains REVERT: B 370 ASN cc_start: 0.7391 (m-40) cc_final: 0.7093 (m-40) outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 0.8630 time to fit residues: 50.5826 Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 38 optimal weight: 0.0570 chunk 27 optimal weight: 0.3980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.148908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.132670 restraints weight = 6201.277| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.93 r_work: 0.3834 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3439 Z= 0.202 Angle : 0.600 11.307 4670 Z= 0.312 Chirality : 0.045 0.154 498 Planarity : 0.004 0.050 604 Dihedral : 5.646 56.241 500 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 1.92 % Allowed : 12.09 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.77 (0.40), residues: 424 helix: -3.51 (0.71), residues: 25 sheet: 0.58 (0.40), residues: 168 loop : -0.99 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE B 515 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4294.50 seconds wall clock time: 76 minutes 20.99 seconds (4580.99 seconds total)