Starting phenix.real_space_refine on Mon Jan 13 16:08:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyg_43660/01_2025/8vyg_43660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyg_43660/01_2025/8vyg_43660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vyg_43660/01_2025/8vyg_43660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyg_43660/01_2025/8vyg_43660.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyg_43660/01_2025/8vyg_43660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyg_43660/01_2025/8vyg_43660.cif" } resolution = 3.1 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= 0.054 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 13 5.16 5 C 2028 2.51 5 N 545 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 3204 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 975 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1420 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" 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: 4.41, per 1000 atoms: 1.38 Number of scatterers: 3204 At special positions: 0 Unit cell: (92.73, 64.068, 80.085, 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 13 16.00 O 618 8.00 N 545 7.00 C 2028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.05 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.05 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 R1301 " - " ASN R 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 705.1 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 13.9% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.540A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.941A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 386 through 389 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.778A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 7.260A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.567A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 120 hydrogen bonds defined for protein. 276 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: 0.78 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 606 1.32 - 1.45: 904 1.45 - 1.58: 1754 1.58 - 1.71: 1 1.71 - 1.84: 16 Bond restraints: 3281 Sorted by residual: bond pdb=" N LEU R 517 " pdb=" CA LEU R 517 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.20e-02 6.94e+03 8.65e+00 bond pdb=" N ARG R 346 " pdb=" CA ARG R 346 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.24e-02 6.50e+03 8.58e+00 bond pdb=" N ILE B 49 " pdb=" CA ILE B 49 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.55e+00 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.19e+00 bond pdb=" N TYR R 449 " pdb=" CA TYR R 449 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.92e+00 ... (remaining 3276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 3737 1.46 - 2.92: 589 2.92 - 4.38: 83 4.38 - 5.84: 33 5.84 - 7.30: 20 Bond angle restraints: 4462 Sorted by residual: angle pdb=" C CYS R 383 " pdb=" N PRO R 384 " pdb=" CA PRO R 384 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 angle pdb=" C GLN R 498 " pdb=" N PRO R 499 " pdb=" CA PRO R 499 " ideal model delta sigma weight residual 119.56 126.70 -7.14 1.01e+00 9.80e-01 4.99e+01 angle pdb=" C ILE B 59 " pdb=" N PRO B 60 " pdb=" CA PRO B 60 " ideal model delta sigma weight residual 119.78 126.92 -7.14 1.03e+00 9.43e-01 4.81e+01 angle pdb=" C SER R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.19 126.46 -7.27 1.06e+00 8.90e-01 4.71e+01 angle pdb=" C ALA R 411 " pdb=" N PRO R 412 " pdb=" CA PRO R 412 " ideal model delta sigma weight residual 119.76 126.78 -7.02 1.03e+00 9.43e-01 4.65e+01 ... (remaining 4457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 1815 13.97 - 27.93: 75 27.93 - 41.90: 28 41.90 - 55.86: 7 55.86 - 69.83: 8 Dihedral angle restraints: 1933 sinusoidal: 744 harmonic: 1189 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 89 " pdb=" CB CYS B 89 " ideal model delta sinusoidal sigma weight residual 93.00 58.37 34.63 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" C ASP R 427 " pdb=" N ASP R 427 " pdb=" CA ASP R 427 " pdb=" CB ASP R 427 " ideal model delta harmonic sigma weight residual -122.60 -131.83 9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C PHE R 377 " pdb=" N PHE R 377 " pdb=" CA PHE R 377 " pdb=" CB PHE R 377 " ideal model delta harmonic sigma weight residual -122.60 -113.75 -8.85 0 2.50e+00 1.60e-01 1.25e+01 ... (remaining 1930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 353 0.069 - 0.138: 103 0.138 - 0.207: 24 0.207 - 0.276: 4 0.276 - 0.345: 3 Chirality restraints: 487 Sorted by residual: chirality pdb=" C2 NAG R1301 " pdb=" C1 NAG R1301 " pdb=" C3 NAG R1301 " pdb=" N2 NAG R1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA TYR R 495 " pdb=" N TYR R 495 " pdb=" C TYR R 495 " pdb=" CB TYR R 495 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASP R 427 " pdb=" N ASP R 427 " pdb=" C ASP R 427 " pdb=" CB ASP R 427 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 484 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " 0.023 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP B 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 377 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C PHE R 377 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE R 377 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS R 378 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 50 " -0.024 2.00e-02 2.50e+03 1.14e-02 3.22e+00 pdb=" CG TRP A 50 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 50 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 50 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 50 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 50 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 50 " -0.012 2.00e-02 2.50e+03 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1656 2.99 - 3.47: 2694 3.47 - 3.95: 5343 3.95 - 4.42: 6021 4.42 - 4.90: 9767 Nonbonded interactions: 25481 Sorted by model distance: nonbonded pdb=" O ASP R 427 " pdb=" OD1 ASP R 427 " model vdw 2.515 3.040 nonbonded pdb=" N ASP R 428 " pdb=" OD1 ASP R 428 " model vdw 2.532 3.120 nonbonded pdb=" O PHE R 377 " pdb=" CB PHE R 377 " model vdw 2.608 2.752 nonbonded pdb=" N GLU B 80 " pdb=" O GLU B 80 " model vdw 2.612 2.496 nonbonded pdb=" N GLY R 416 " pdb=" O GLY R 416 " model vdw 2.615 2.496 ... (remaining 25476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 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: 0.210 Process input model: 14.520 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.010 0.054 3281 Z= 0.673 Angle : 1.217 7.296 4462 Z= 0.839 Chirality : 0.073 0.345 487 Planarity : 0.005 0.018 577 Dihedral : 10.292 69.829 1166 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.30 % Allowed : 0.60 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.68 (0.41), residues: 408 helix: -4.23 (0.43), residues: 31 sheet: 1.32 (0.42), residues: 144 loop : 0.69 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.014 0.003 PHE R 497 TYR 0.017 0.003 TYR A 95 ARG 0.002 0.000 ARG R 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.321 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1953 time to fit residues: 23.6367 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 116 ASN B 6 GLN B 90 GLN B 92 HIS R 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140934 restraints weight = 5897.969| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.80 r_work: 0.3739 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3281 Z= 0.215 Angle : 0.554 3.761 4462 Z= 0.303 Chirality : 0.045 0.141 487 Planarity : 0.005 0.027 577 Dihedral : 4.320 24.844 480 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.99 % Allowed : 10.75 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.81 (0.42), residues: 408 helix: -4.00 (0.68), residues: 27 sheet: 1.46 (0.43), residues: 154 loop : 0.58 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE R 377 TYR 0.016 0.002 TYR B 87 ARG 0.004 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.362 Fit side-chains REVERT: A 23 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7001 (tppt) REVERT: A 47 TRP cc_start: 0.7678 (t60) cc_final: 0.7444 (t60) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.2030 time to fit residues: 16.4016 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 6 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134800 restraints weight = 5812.576| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.54 r_work: 0.3658 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3281 Z= 0.341 Angle : 0.685 7.635 4462 Z= 0.361 Chirality : 0.048 0.142 487 Planarity : 0.006 0.040 577 Dihedral : 5.318 28.501 480 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.18 % Allowed : 14.03 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.42), residues: 408 helix: -4.01 (0.70), residues: 26 sheet: 1.19 (0.42), residues: 155 loop : 0.09 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.023 0.002 PHE R 377 TYR 0.018 0.003 TYR A 60 ARG 0.004 0.001 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.325 Fit side-chains REVERT: A 23 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7321 (tppt) REVERT: A 47 TRP cc_start: 0.7791 (t60) cc_final: 0.7547 (t60) REVERT: R 444 LYS cc_start: 0.6754 (ptpt) cc_final: 0.6406 (pttp) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.2055 time to fit residues: 17.0152 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 43 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.170234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138411 restraints weight = 5917.433| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.57 r_work: 0.3707 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3281 Z= 0.146 Angle : 0.500 6.233 4462 Z= 0.267 Chirality : 0.043 0.140 487 Planarity : 0.005 0.037 577 Dihedral : 4.435 24.923 480 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.09 % Allowed : 15.22 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.23 (0.42), residues: 408 helix: -3.91 (0.69), residues: 26 sheet: 0.92 (0.40), residues: 168 loop : 0.16 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE B 72 TYR 0.027 0.002 TYR A 27 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.336 Fit side-chains REVERT: A 23 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7379 (tppt) REVERT: A 50 TRP cc_start: 0.7654 (t60) cc_final: 0.7397 (t60) REVERT: R 346 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7441 (mtp85) REVERT: R 369 TYR cc_start: 0.6308 (t80) cc_final: 0.5800 (t80) REVERT: R 444 LYS cc_start: 0.6722 (ptpt) cc_final: 0.6363 (pttp) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1921 time to fit residues: 13.1840 Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 38 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.169238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137413 restraints weight = 5828.785| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.52 r_work: 0.3702 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3281 Z= 0.190 Angle : 0.516 6.075 4462 Z= 0.273 Chirality : 0.044 0.150 487 Planarity : 0.005 0.039 577 Dihedral : 4.531 26.487 480 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.99 % Allowed : 15.52 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.42), residues: 408 helix: -3.83 (0.71), residues: 26 sheet: 0.83 (0.40), residues: 166 loop : 0.11 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE R 377 TYR 0.020 0.002 TYR A 27 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.358 Fit side-chains REVERT: A 23 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7347 (tppt) REVERT: A 50 TRP cc_start: 0.7647 (t60) cc_final: 0.7410 (t60) REVERT: R 346 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7395 (mtp85) REVERT: R 369 TYR cc_start: 0.6263 (t80) cc_final: 0.5831 (t80) REVERT: R 444 LYS cc_start: 0.6717 (ptpt) cc_final: 0.6415 (pttp) outliers start: 10 outliers final: 10 residues processed: 53 average time/residue: 0.1809 time to fit residues: 11.5679 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142116 restraints weight = 5979.656| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.41 r_work: 0.3711 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3281 Z= 0.175 Angle : 0.504 6.532 4462 Z= 0.265 Chirality : 0.044 0.140 487 Planarity : 0.005 0.040 577 Dihedral : 4.446 25.688 480 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.88 % Allowed : 14.33 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.12 (0.42), residues: 408 helix: -3.77 (0.73), residues: 26 sheet: 0.83 (0.41), residues: 168 loop : 0.08 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE B 72 TYR 0.018 0.002 TYR A 27 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.368 Fit side-chains REVERT: A 23 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7371 (tppt) REVERT: R 369 TYR cc_start: 0.6303 (t80) cc_final: 0.5889 (t80) REVERT: R 444 LYS cc_start: 0.6683 (ptpt) cc_final: 0.6403 (pttp) outliers start: 13 outliers final: 12 residues processed: 55 average time/residue: 0.1739 time to fit residues: 11.6979 Evaluate side-chains 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137654 restraints weight = 5891.191| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.50 r_work: 0.3704 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3281 Z= 0.186 Angle : 0.516 6.244 4462 Z= 0.270 Chirality : 0.044 0.141 487 Planarity : 0.005 0.041 577 Dihedral : 4.440 26.006 480 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.18 % Allowed : 15.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.14 (0.42), residues: 408 helix: -3.79 (0.71), residues: 26 sheet: 0.95 (0.41), residues: 165 loop : 0.00 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 47 HIS 0.002 0.001 HIS B 92 PHE 0.014 0.001 PHE B 72 TYR 0.020 0.002 TYR A 54 ARG 0.004 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.344 Fit side-chains REVERT: A 23 LYS cc_start: 0.7809 (ttmm) cc_final: 0.7305 (tppt) REVERT: B 43 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: R 369 TYR cc_start: 0.6351 (t80) cc_final: 0.5950 (t80) REVERT: R 444 LYS cc_start: 0.6675 (ptpt) cc_final: 0.6310 (pttp) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.1965 time to fit residues: 12.4822 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136364 restraints weight = 5959.492| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.47 r_work: 0.3690 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3281 Z= 0.255 Angle : 0.577 8.031 4462 Z= 0.300 Chirality : 0.046 0.148 487 Planarity : 0.005 0.042 577 Dihedral : 4.776 27.462 480 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.18 % Allowed : 15.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.01 (0.42), residues: 408 helix: -3.85 (0.71), residues: 26 sheet: 0.84 (0.41), residues: 166 loop : -0.10 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 47 HIS 0.003 0.002 HIS B 92 PHE 0.019 0.002 PHE B 72 TYR 0.019 0.002 TYR A 54 ARG 0.006 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.364 Fit side-chains REVERT: A 23 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7416 (tppt) REVERT: B 43 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: R 444 LYS cc_start: 0.6774 (ptpt) cc_final: 0.6509 (pttp) outliers start: 14 outliers final: 12 residues processed: 55 average time/residue: 0.1890 time to fit residues: 12.4686 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 0.0020 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138011 restraints weight = 5891.270| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.47 r_work: 0.3713 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3281 Z= 0.163 Angle : 0.523 7.766 4462 Z= 0.273 Chirality : 0.044 0.140 487 Planarity : 0.005 0.041 577 Dihedral : 4.451 25.056 480 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.18 % Allowed : 16.42 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.42), residues: 408 helix: -3.82 (0.70), residues: 26 sheet: 0.98 (0.41), residues: 165 loop : -0.04 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.012 0.001 PHE B 72 TYR 0.018 0.002 TYR A 54 ARG 0.007 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7403 (tppt) REVERT: R 369 TYR cc_start: 0.6331 (t80) cc_final: 0.5927 (t80) REVERT: R 444 LYS cc_start: 0.6759 (ptpt) cc_final: 0.6482 (pttp) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.2029 time to fit residues: 12.9819 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.170046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139328 restraints weight = 5850.694| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.48 r_work: 0.3728 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3281 Z= 0.138 Angle : 0.522 10.530 4462 Z= 0.269 Chirality : 0.044 0.138 487 Planarity : 0.005 0.042 577 Dihedral : 4.240 24.336 480 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.99 % Allowed : 18.21 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.29 (0.43), residues: 408 helix: -3.69 (0.71), residues: 26 sheet: 1.06 (0.41), residues: 168 loop : 0.09 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 36 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE B 72 TYR 0.022 0.002 TYR A 54 ARG 0.007 0.000 ARG R 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7444 (tppt) REVERT: B 43 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: R 369 TYR cc_start: 0.6247 (t80) cc_final: 0.5838 (t80) REVERT: R 444 LYS cc_start: 0.6743 (ptpt) cc_final: 0.6489 (pttp) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.1735 time to fit residues: 11.8616 Evaluate side-chains 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140334 restraints weight = 5779.722| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.45 r_work: 0.3745 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3281 Z= 0.130 Angle : 0.511 8.983 4462 Z= 0.267 Chirality : 0.043 0.138 487 Planarity : 0.005 0.042 577 Dihedral : 4.106 24.028 480 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.69 % Allowed : 18.21 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.39 (0.43), residues: 408 helix: -3.64 (0.72), residues: 26 sheet: 1.12 (0.41), residues: 168 loop : 0.15 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 36 HIS 0.001 0.001 HIS B 92 PHE 0.010 0.001 PHE B 72 TYR 0.021 0.002 TYR A 54 ARG 0.007 0.000 ARG R 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.98 seconds wall clock time: 45 minutes 56.37 seconds (2756.37 seconds total)