Starting phenix.real_space_refine on Sat Apr 26 19:20:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyg_43660/04_2025/8vyg_43660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyg_43660/04_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_43660/04_2025/8vyg_43660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyg_43660/04_2025/8vyg_43660.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyg_43660/04_2025/8vyg_43660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyg_43660/04_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-5669/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: 4.70, per 1000 atoms: 1.47 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: 0.77 Conformation dependent library (CDL) restraints added in 410.4 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: 0.42 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: 0.82 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 5.890 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.460 Find NCS groups from input model: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.05155 ( 1) link_NAG-ASN : angle 2.56796 ( 3) hydrogen bonds : bond 0.17884 ( 116) hydrogen bonds : angle 8.65630 ( 276) SS BOND : bond 0.01385 ( 5) SS BOND : angle 2.33171 ( 10) covalent geometry : bond 0.01018 ( 3281) covalent geometry : angle 1.21651 ( 4462) *********************** 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 : 0.343 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1875 time to fit residues: 22.7681 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 : 0.335 ------------------------------------------------------------------------------- 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: 5.9990 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 = 46)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140846 restraints weight = 5897.969| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.82 r_work: 0.3738 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 3287 Z= 0.145 Angle : 0.556 3.761 4475 Z= 0.304 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 1) link_NAG-ASN : angle 1.56636 ( 3) hydrogen bonds : bond 0.04057 ( 116) hydrogen bonds : angle 6.16922 ( 276) SS BOND : bond 0.00491 ( 5) SS BOND : angle 0.93494 ( 10) covalent geometry : bond 0.00328 ( 3281) covalent geometry : angle 0.55364 ( 4462) *********************** 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 : 0.343 Fit side-chains REVERT: A 23 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6992 (tppt) REVERT: A 47 TRP cc_start: 0.7670 (t60) cc_final: 0.7430 (t60) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.1994 time to fit residues: 16.0304 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 : 0.363 ------------------------------------------------------------------------------- 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: 0.9980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.169836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138006 restraints weight = 5839.373| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.62 r_work: 0.3696 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3287 Z= 0.144 Angle : 0.549 5.343 4475 Z= 0.294 Chirality : 0.044 0.138 487 Planarity : 0.005 0.041 577 Dihedral : 4.438 26.135 480 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.88 % Allowed : 13.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.42), residues: 408 helix: -3.91 (0.72), residues: 26 sheet: 1.33 (0.42), residues: 154 loop : 0.29 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.012 0.001 PHE R 377 TYR 0.017 0.002 TYR A 60 ARG 0.004 0.001 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 1.86555 ( 3) hydrogen bonds : bond 0.03732 ( 116) hydrogen bonds : angle 6.01400 ( 276) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.30346 ( 10) covalent geometry : bond 0.00331 ( 3281) covalent geometry : angle 0.54370 ( 4462) *********************** 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 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.377 Fit side-chains REVERT: A 23 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7258 (tppt) REVERT: R 444 LYS cc_start: 0.6660 (ptpt) cc_final: 0.6384 (pttp) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.2060 time to fit residues: 15.2717 Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain A residue 81 MET 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: 5.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- 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 43 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136868 restraints weight = 5939.039| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.59 r_work: 0.3688 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3287 Z= 0.161 Angle : 0.569 5.460 4475 Z= 0.299 Chirality : 0.045 0.141 487 Planarity : 0.005 0.039 577 Dihedral : 4.690 26.686 480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.28 % Allowed : 13.43 % Favored : 83.28 % 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: 0.43 (0.43), residues: 408 helix: -3.84 (0.72), residues: 26 sheet: 1.04 (0.41), residues: 166 loop : 0.34 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 436 HIS 0.001 0.000 HIS B 92 PHE 0.014 0.002 PHE R 377 TYR 0.012 0.002 TYR R 369 ARG 0.006 0.001 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 1.99717 ( 3) hydrogen bonds : bond 0.03658 ( 116) hydrogen bonds : angle 6.12638 ( 276) SS BOND : bond 0.00353 ( 5) SS BOND : angle 1.43827 ( 10) covalent geometry : bond 0.00374 ( 3281) covalent geometry : angle 0.56324 ( 4462) *********************** 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 67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.335 Fit side-chains REVERT: A 23 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7374 (tppt) REVERT: R 444 LYS cc_start: 0.6737 (ptpt) cc_final: 0.6375 (pttp) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.2078 time to fit residues: 14.1878 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 : 0.367 ------------------------------------------------------------------------------- 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 80 TYR Chi-restraints excluded: chain A residue 81 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.170320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138519 restraints weight = 5855.465| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.55 r_work: 0.3712 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3287 Z= 0.106 Angle : 0.499 5.912 4475 Z= 0.263 Chirality : 0.043 0.140 487 Planarity : 0.005 0.039 577 Dihedral : 4.320 25.161 480 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.69 % Allowed : 15.82 % 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: 0.30 (0.43), residues: 408 helix: -3.77 (0.72), residues: 26 sheet: 0.88 (0.41), residues: 169 loop : 0.28 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.015 0.001 PHE B 72 TYR 0.009 0.001 TYR A 80 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 1.68485 ( 3) hydrogen bonds : bond 0.03184 ( 116) hydrogen bonds : angle 5.91192 ( 276) SS BOND : bond 0.00160 ( 5) SS BOND : angle 1.08875 ( 10) covalent geometry : bond 0.00241 ( 3281) covalent geometry : angle 0.49523 ( 4462) *********************** 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 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.375 Fit side-chains REVERT: A 23 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7374 (tppt) REVERT: R 346 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7395 (mtp85) REVERT: R 369 TYR cc_start: 0.6284 (t80) cc_final: 0.5891 (t80) REVERT: R 444 LYS cc_start: 0.6717 (ptpt) cc_final: 0.6399 (pttp) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1766 time to fit residues: 11.6969 Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 45 LEU 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 B residue 57 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: 0.7980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.166312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134544 restraints weight = 5959.188| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.54 r_work: 0.3655 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3287 Z= 0.221 Angle : 0.642 7.423 4475 Z= 0.332 Chirality : 0.047 0.215 487 Planarity : 0.005 0.040 577 Dihedral : 5.208 29.250 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.18 % Allowed : 14.33 % 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: -0.08 (0.41), residues: 408 helix: -3.88 (0.71), residues: 26 sheet: 0.72 (0.40), residues: 166 loop : -0.08 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.020 0.002 PHE R 377 TYR 0.020 0.002 TYR A 54 ARG 0.002 0.001 ARG R 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 1) link_NAG-ASN : angle 2.44783 ( 3) hydrogen bonds : bond 0.03922 ( 116) hydrogen bonds : angle 6.43375 ( 276) SS BOND : bond 0.00494 ( 5) SS BOND : angle 1.23848 ( 10) covalent geometry : bond 0.00518 ( 3281) covalent geometry : angle 0.63724 ( 4462) *********************** 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 69 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.366 Fit side-chains REVERT: A 23 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7418 (tppt) REVERT: R 444 LYS cc_start: 0.6785 (ptpt) cc_final: 0.6446 (pttp) outliers start: 14 outliers final: 12 residues processed: 60 average time/residue: 0.1732 time to fit residues: 12.5126 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.0050 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4272 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.170345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139146 restraints weight = 5841.027| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.48 r_work: 0.3724 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3287 Z= 0.096 Angle : 0.505 7.032 4475 Z= 0.263 Chirality : 0.044 0.140 487 Planarity : 0.005 0.039 577 Dihedral : 4.334 24.002 480 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.69 % Allowed : 17.31 % 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: 0.09 (0.42), residues: 408 helix: -3.79 (0.71), residues: 26 sheet: 0.80 (0.41), residues: 169 loop : 0.06 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 47 HIS 0.001 0.000 HIS B 92 PHE 0.013 0.001 PHE B 72 TYR 0.033 0.002 TYR A 27 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 1.73015 ( 3) hydrogen bonds : bond 0.03099 ( 116) hydrogen bonds : angle 5.97841 ( 276) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.88257 ( 10) covalent geometry : bond 0.00217 ( 3281) covalent geometry : angle 0.50178 ( 4462) *********************** 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 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.364 Fit side-chains REVERT: A 23 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7448 (tppt) REVERT: A 36 TRP cc_start: 0.7951 (m100) cc_final: 0.7703 (m100) REVERT: R 346 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7382 (mtp85) REVERT: R 369 TYR cc_start: 0.6277 (t80) cc_final: 0.5855 (t80) REVERT: R 444 LYS cc_start: 0.6702 (ptpt) cc_final: 0.6407 (pttp) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.2000 time to fit residues: 12.8455 Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain R residue 389 ASP 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: 1.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.169800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138860 restraints weight = 5902.492| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.50 r_work: 0.3718 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5759 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= 0.106 Angle : 0.517 9.107 4475 Z= 0.267 Chirality : 0.044 0.140 487 Planarity : 0.004 0.039 577 Dihedral : 4.242 25.486 480 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.39 % Allowed : 18.81 % 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: 0.26 (0.43), residues: 408 helix: -3.69 (0.72), residues: 26 sheet: 1.00 (0.42), residues: 166 loop : 0.11 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 47 HIS 0.001 0.000 HIS B 92 PHE 0.014 0.001 PHE R 497 TYR 0.028 0.002 TYR A 27 ARG 0.001 0.000 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.68685 ( 3) hydrogen bonds : bond 0.03130 ( 116) hydrogen bonds : angle 5.95928 ( 276) SS BOND : bond 0.00240 ( 5) SS BOND : angle 0.88665 ( 10) covalent geometry : bond 0.00241 ( 3281) covalent geometry : angle 0.51412 ( 4462) *********************** 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 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.367 Fit side-chains REVERT: A 23 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7377 (tppt) REVERT: A 38 ARG cc_start: 0.5844 (tmm-80) cc_final: 0.5577 (tmm-80) REVERT: R 346 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7415 (mtp85) REVERT: R 369 TYR cc_start: 0.6288 (t80) cc_final: 0.5923 (t80) REVERT: R 444 LYS cc_start: 0.6749 (ptpt) cc_final: 0.6470 (pttp) outliers start: 8 outliers final: 7 residues processed: 52 average time/residue: 0.1963 time to fit residues: 12.1693 Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.167679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136486 restraints weight = 5865.941| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.47 r_work: 0.3690 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3287 Z= 0.172 Angle : 0.613 11.126 4475 Z= 0.308 Chirality : 0.046 0.139 487 Planarity : 0.005 0.040 577 Dihedral : 4.800 27.401 480 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.28 % Allowed : 17.91 % 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: 0.05 (0.42), residues: 408 helix: -3.80 (0.72), residues: 26 sheet: 0.88 (0.41), residues: 166 loop : -0.06 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 47 HIS 0.003 0.002 HIS B 92 PHE 0.021 0.002 PHE B 72 TYR 0.029 0.002 TYR A 27 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 2.13081 ( 3) hydrogen bonds : bond 0.03603 ( 116) hydrogen bonds : angle 6.28188 ( 276) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.04525 ( 10) covalent geometry : bond 0.00403 ( 3281) covalent geometry : angle 0.60956 ( 4462) *********************** 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 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.355 Fit side-chains REVERT: A 23 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7381 (tppt) REVERT: A 38 ARG cc_start: 0.5656 (tmm-80) cc_final: 0.5450 (tmm-80) REVERT: A 50 TRP cc_start: 0.7742 (t60) cc_final: 0.7468 (t60) REVERT: R 444 LYS cc_start: 0.6788 (ptpt) cc_final: 0.6475 (pttp) outliers start: 11 outliers final: 11 residues processed: 54 average time/residue: 0.2018 time to fit residues: 12.8355 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 364 ASP 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: 4.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 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 B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137757 restraints weight = 5854.914| |-----------------------------------------------------------------------------| 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: 0.7636 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3287 Z= 0.129 Angle : 0.568 10.318 4475 Z= 0.287 Chirality : 0.045 0.141 487 Planarity : 0.005 0.044 577 Dihedral : 4.547 25.297 480 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.29 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: 0.13 (0.42), residues: 408 helix: -3.80 (0.70), residues: 26 sheet: 0.95 (0.41), residues: 166 loop : -0.01 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 47 HIS 0.001 0.000 HIS B 92 PHE 0.016 0.001 PHE B 72 TYR 0.028 0.002 TYR A 27 ARG 0.001 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 1.89763 ( 3) hydrogen bonds : bond 0.03327 ( 116) hydrogen bonds : angle 6.22613 ( 276) SS BOND : bond 0.00296 ( 5) SS BOND : angle 1.00394 ( 10) covalent geometry : bond 0.00298 ( 3281) covalent geometry : angle 0.56514 ( 4462) ********************** 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 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.393 Fit side-chains REVERT: A 23 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7433 (tppt) REVERT: A 38 ARG cc_start: 0.5583 (tmm-80) cc_final: 0.5371 (tmm-80) REVERT: A 50 TRP cc_start: 0.7706 (t60) cc_final: 0.7379 (t60) REVERT: B 28 THR cc_start: 0.6897 (m) cc_final: 0.6695 (t) REVERT: R 369 TYR cc_start: 0.6314 (t80) cc_final: 0.5943 (t80) REVERT: R 444 LYS cc_start: 0.6755 (ptpt) cc_final: 0.6442 (pttp) outliers start: 9 outliers final: 9 residues processed: 53 average time/residue: 0.1991 time to fit residues: 12.6076 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.169663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138598 restraints weight = 5829.046| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.52 r_work: 0.3708 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6033 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= 0.118 Angle : 0.553 9.117 4475 Z= 0.281 Chirality : 0.044 0.140 487 Planarity : 0.005 0.041 577 Dihedral : 4.420 24.692 480 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.39 % Allowed : 17.91 % Favored : 79.70 % 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: 0.22 (0.43), residues: 408 helix: -3.75 (0.71), residues: 26 sheet: 1.04 (0.42), residues: 166 loop : 0.02 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 47 HIS 0.001 0.001 HIS B 92 PHE 0.014 0.001 PHE B 72 TYR 0.026 0.002 TYR A 27 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 1.77397 ( 3) hydrogen bonds : bond 0.03233 ( 116) hydrogen bonds : angle 6.19647 ( 276) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.93348 ( 10) covalent geometry : bond 0.00272 ( 3281) covalent geometry : angle 0.54994 ( 4462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.46 seconds wall clock time: 45 minutes 31.45 seconds (2731.45 seconds total)