Starting phenix.real_space_refine on Wed Sep 17 03:31:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyg_43660/09_2025/8vyg_43660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyg_43660/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vyg_43660/09_2025/8vyg_43660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyg_43660/09_2025/8vyg_43660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vyg_43660/09_2025/8vyg_43660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyg_43660/09_2025/8vyg_43660.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASN:plan1': 2, 'GLU:plan': 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: 0.91, per 1000 atoms: 0.28 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: 0.26 Conformation dependent library (CDL) restraints added in 130.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.12 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: 0.41 Time building geometry restraints manager: 0.36 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: 8.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.890 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- 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 3287 Z= 0.593 Angle : 1.222 7.296 4475 Z= 0.840 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG R 466 TYR 0.017 0.003 TYR A 95 PHE 0.014 0.003 PHE R 497 TRP 0.024 0.006 TRP A 50 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.01018 ( 3281) covalent geometry : angle 1.21651 ( 4462) SS BOND : bond 0.01385 ( 5) SS BOND : angle 2.33171 ( 10) hydrogen bonds : bond 0.17884 ( 116) hydrogen bonds : angle 8.65630 ( 276) link_NAG-ASN : bond 0.05155 ( 1) link_NAG-ASN : angle 2.56796 ( 3) *********************** 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 : 0.125 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.0801 time to fit residues: 9.7888 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.173457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140605 restraints weight = 5962.497| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.82 r_work: 0.3737 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3287 Z= 0.150 Angle : 0.568 3.931 4475 Z= 0.309 Chirality : 0.045 0.139 487 Planarity : 0.005 0.027 577 Dihedral : 4.379 24.813 480 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.42), residues: 408 helix: -3.97 (0.70), residues: 27 sheet: 1.43 (0.43), residues: 154 loop : 0.58 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 18 TYR 0.014 0.002 TYR B 87 PHE 0.010 0.002 PHE R 377 TRP 0.015 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3281) covalent geometry : angle 0.56536 ( 4462) SS BOND : bond 0.00364 ( 5) SS BOND : angle 0.95185 ( 10) hydrogen bonds : bond 0.04067 ( 116) hydrogen bonds : angle 6.12652 ( 276) link_NAG-ASN : bond 0.00395 ( 1) link_NAG-ASN : angle 1.69941 ( 3) *********************** 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 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.135 Fit side-chains REVERT: A 23 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7131 (tppt) REVERT: A 47 TRP cc_start: 0.7656 (t60) cc_final: 0.7431 (t60) REVERT: R 441 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7998 (tt) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.0899 time to fit residues: 7.1918 Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 39 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.170231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138533 restraints weight = 5942.285| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.62 r_work: 0.3705 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3287 Z= 0.129 Angle : 0.523 4.884 4475 Z= 0.280 Chirality : 0.044 0.139 487 Planarity : 0.005 0.039 577 Dihedral : 4.350 26.099 480 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.48 % Allowed : 12.54 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.42), residues: 408 helix: -3.89 (0.71), residues: 26 sheet: 1.16 (0.41), residues: 164 loop : 0.34 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 346 TYR 0.017 0.002 TYR A 60 PHE 0.011 0.001 PHE R 377 TRP 0.014 0.001 TRP R 436 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3281) covalent geometry : angle 0.51881 ( 4462) SS BOND : bond 0.00607 ( 5) SS BOND : angle 1.20008 ( 10) hydrogen bonds : bond 0.03565 ( 116) hydrogen bonds : angle 5.93476 ( 276) link_NAG-ASN : bond 0.00119 ( 1) link_NAG-ASN : angle 1.71434 ( 3) *********************** 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: 15 poor density : 66 time to evaluate : 0.083 Fit side-chains REVERT: A 23 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7376 (tppt) REVERT: R 346 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7517 (mtm-85) REVERT: R 356 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7977 (ttmm) REVERT: R 441 LEU cc_start: 0.8324 (tp) cc_final: 0.8037 (tt) REVERT: R 444 LYS cc_start: 0.6648 (ptpt) cc_final: 0.6395 (pttp) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.0817 time to fit residues: 6.7691 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 34 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 465 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.170207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139490 restraints weight = 5901.047| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.74 r_work: 0.3697 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3287 Z= 0.129 Angle : 0.521 4.536 4475 Z= 0.277 Chirality : 0.044 0.138 487 Planarity : 0.005 0.039 577 Dihedral : 4.413 26.187 480 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.99 % Allowed : 14.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.42), residues: 408 helix: -3.82 (0.71), residues: 26 sheet: 1.10 (0.41), residues: 164 loop : 0.25 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.016 0.002 TYR R 380 PHE 0.011 0.001 PHE R 377 TRP 0.012 0.002 TRP R 436 HIS 0.001 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3281) covalent geometry : angle 0.51555 ( 4462) SS BOND : bond 0.00432 ( 5) SS BOND : angle 1.34368 ( 10) hydrogen bonds : bond 0.03405 ( 116) hydrogen bonds : angle 5.91871 ( 276) link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.76905 ( 3) *********************** 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: 10 poor density : 54 time to evaluate : 0.083 Fit side-chains REVERT: A 23 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7380 (tppt) REVERT: R 356 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: R 444 LYS cc_start: 0.6809 (ptpt) cc_final: 0.6483 (pttp) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0752 time to fit residues: 5.0635 Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133931 restraints weight = 5890.853| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.49 r_work: 0.3648 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3287 Z= 0.257 Angle : 0.693 8.111 4475 Z= 0.358 Chirality : 0.048 0.148 487 Planarity : 0.006 0.039 577 Dihedral : 5.469 30.069 480 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.78 % Allowed : 13.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.41), residues: 408 helix: -3.99 (0.69), residues: 26 sheet: 0.76 (0.40), residues: 166 loop : -0.17 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 346 TYR 0.016 0.002 TYR R 380 PHE 0.024 0.003 PHE R 377 TRP 0.022 0.003 TRP A 47 HIS 0.001 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 3281) covalent geometry : angle 0.68597 ( 4462) SS BOND : bond 0.00444 ( 5) SS BOND : angle 1.68895 ( 10) hydrogen bonds : bond 0.04188 ( 116) hydrogen bonds : angle 6.55189 ( 276) link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 2.60421 ( 3) *********************** 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 75 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.110 Fit side-chains REVERT: A 23 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7424 (tppt) REVERT: A 38 ARG cc_start: 0.6009 (tmm-80) cc_final: 0.5758 (tmm-80) REVERT: A 47 TRP cc_start: 0.7877 (t60) cc_final: 0.7649 (t60) REVERT: A 122 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6381 (mm) REVERT: R 356 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7952 (ttmm) REVERT: R 364 ASP cc_start: 0.7341 (t0) cc_final: 0.7042 (m-30) REVERT: R 444 LYS cc_start: 0.6753 (ptpt) cc_final: 0.6413 (pttp) outliers start: 16 outliers final: 12 residues processed: 63 average time/residue: 0.0897 time to fit residues: 6.5776 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 48 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 356 LYS 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 25 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135977 restraints weight = 5875.540| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.49 r_work: 0.3684 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3287 Z= 0.161 Angle : 0.586 7.543 4475 Z= 0.302 Chirality : 0.045 0.142 487 Planarity : 0.005 0.037 577 Dihedral : 4.952 27.664 480 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.18 % Allowed : 15.52 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.41), residues: 408 helix: -3.91 (0.70), residues: 26 sheet: 0.67 (0.40), residues: 166 loop : -0.21 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.035 0.002 TYR A 27 PHE 0.014 0.002 PHE R 377 TRP 0.014 0.002 TRP R 436 HIS 0.001 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3281) covalent geometry : angle 0.58111 ( 4462) SS BOND : bond 0.00293 ( 5) SS BOND : angle 1.28697 ( 10) hydrogen bonds : bond 0.03608 ( 116) hydrogen bonds : angle 6.40335 ( 276) link_NAG-ASN : bond 0.00146 ( 1) link_NAG-ASN : angle 2.15869 ( 3) *********************** 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 67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.130 Fit side-chains REVERT: A 23 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7454 (tppt) REVERT: R 346 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.7395 (mtp85) REVERT: R 356 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7929 (ttmm) REVERT: R 444 LYS cc_start: 0.6794 (ptpt) cc_final: 0.6455 (pttp) outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.0988 time to fit residues: 6.5331 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.167679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136321 restraints weight = 5976.993| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.49 r_work: 0.3686 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3287 Z= 0.156 Angle : 0.579 6.860 4475 Z= 0.301 Chirality : 0.046 0.142 487 Planarity : 0.005 0.039 577 Dihedral : 4.870 27.396 480 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.78 % Allowed : 14.63 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.42), residues: 408 helix: -3.90 (0.70), residues: 26 sheet: 0.63 (0.40), residues: 166 loop : -0.23 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.017 0.002 TYR A 54 PHE 0.017 0.002 PHE B 72 TRP 0.020 0.002 TRP A 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3281) covalent geometry : angle 0.57535 ( 4462) SS BOND : bond 0.00342 ( 5) SS BOND : angle 1.10617 ( 10) hydrogen bonds : bond 0.03564 ( 116) hydrogen bonds : angle 6.30382 ( 276) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 2.08520 ( 3) *********************** 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 67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.086 Fit side-chains REVERT: A 23 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7445 (tppt) REVERT: R 346 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7378 (mtp85) REVERT: R 356 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7866 (ttmm) REVERT: R 444 LYS cc_start: 0.6765 (ptpt) cc_final: 0.6472 (pttp) outliers start: 16 outliers final: 13 residues processed: 57 average time/residue: 0.0915 time to fit residues: 6.0804 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 80 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 364 ASP 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 9 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.169243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138028 restraints weight = 5901.153| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.45 r_work: 0.3713 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3287 Z= 0.113 Angle : 0.535 7.761 4475 Z= 0.279 Chirality : 0.044 0.140 487 Planarity : 0.005 0.040 577 Dihedral : 4.521 25.525 480 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.69 % Allowed : 16.42 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.42), residues: 408 helix: -3.85 (0.70), residues: 26 sheet: 0.80 (0.40), residues: 165 loop : -0.17 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.016 0.002 TYR A 54 PHE 0.013 0.001 PHE B 72 TRP 0.018 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3281) covalent geometry : angle 0.53229 ( 4462) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.84923 ( 10) hydrogen bonds : bond 0.03310 ( 116) hydrogen bonds : angle 6.18255 ( 276) link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 1.83316 ( 3) *********************** 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 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7458 (tppt) REVERT: A 36 TRP cc_start: 0.7927 (m100) cc_final: 0.7692 (m100) REVERT: R 346 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.7413 (mtp85) REVERT: R 356 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7843 (ttmm) REVERT: R 369 TYR cc_start: 0.6340 (t80) cc_final: 0.6036 (t80) REVERT: R 444 LYS cc_start: 0.6768 (ptpt) cc_final: 0.6494 (pttp) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.0875 time to fit residues: 5.7839 Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 393 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.170111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139186 restraints weight = 5888.108| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.42 r_work: 0.3726 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3287 Z= 0.105 Angle : 0.533 10.441 4475 Z= 0.274 Chirality : 0.044 0.139 487 Planarity : 0.005 0.041 577 Dihedral : 4.358 25.096 480 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.39 % Allowed : 17.31 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.43), residues: 408 helix: -3.81 (0.70), residues: 26 sheet: 0.90 (0.41), residues: 165 loop : -0.05 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.021 0.002 TYR A 54 PHE 0.012 0.001 PHE B 72 TRP 0.019 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3281) covalent geometry : angle 0.53095 ( 4462) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.79666 ( 10) hydrogen bonds : bond 0.03191 ( 116) hydrogen bonds : angle 6.07552 ( 276) link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 1.72126 ( 3) *********************** 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 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.130 Fit side-chains REVERT: A 23 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7452 (tppt) REVERT: A 36 TRP cc_start: 0.7884 (m100) cc_final: 0.7658 (m100) REVERT: R 346 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.7369 (mtp85) REVERT: R 356 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7818 (ttmm) REVERT: R 369 TYR cc_start: 0.6241 (t80) cc_final: 0.5922 (t80) REVERT: R 444 LYS cc_start: 0.6793 (ptpt) cc_final: 0.6496 (pttp) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.0946 time to fit residues: 5.9665 Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 R residue 356 LYS Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.170077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139147 restraints weight = 5862.426| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.42 r_work: 0.3721 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3287 Z= 0.115 Angle : 0.554 9.212 4475 Z= 0.282 Chirality : 0.044 0.140 487 Planarity : 0.005 0.042 577 Dihedral : 4.370 25.275 480 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.79 % Allowed : 17.61 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.43), residues: 408 helix: -3.69 (0.72), residues: 26 sheet: 0.85 (0.41), residues: 168 loop : -0.01 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.021 0.002 TYR A 54 PHE 0.012 0.001 PHE B 72 TRP 0.019 0.002 TRP A 47 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3281) covalent geometry : angle 0.55140 ( 4462) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.85553 ( 10) hydrogen bonds : bond 0.03216 ( 116) hydrogen bonds : angle 6.07994 ( 276) link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.72710 ( 3) ********************** 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 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.115 Fit side-chains REVERT: A 23 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7424 (tppt) REVERT: A 36 TRP cc_start: 0.7867 (m100) cc_final: 0.7609 (m100) REVERT: A 38 ARG cc_start: 0.5597 (tmm-80) cc_final: 0.5349 (tmm-80) REVERT: R 346 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7384 (mtp85) REVERT: R 369 TYR cc_start: 0.6279 (t80) cc_final: 0.5959 (t80) REVERT: R 444 LYS cc_start: 0.6868 (ptpt) cc_final: 0.6548 (pttp) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.0814 time to fit residues: 4.8764 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 : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 393 THR 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 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.168258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137328 restraints weight = 5987.379| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.45 r_work: 0.3700 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3287 Z= 0.148 Angle : 0.597 8.857 4475 Z= 0.301 Chirality : 0.045 0.143 487 Planarity : 0.005 0.042 577 Dihedral : 4.674 26.233 480 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.09 % Allowed : 17.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.42), residues: 408 helix: -3.73 (0.73), residues: 26 sheet: 0.94 (0.41), residues: 165 loop : -0.13 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.021 0.002 TYR A 54 PHE 0.016 0.002 PHE B 72 TRP 0.022 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3281) covalent geometry : angle 0.59391 ( 4462) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.94052 ( 10) hydrogen bonds : bond 0.03467 ( 116) hydrogen bonds : angle 6.27219 ( 276) link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.96560 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1264.58 seconds wall clock time: 22 minutes 19.71 seconds (1339.71 seconds total)