Starting phenix.real_space_refine on Fri May 9 16:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyg_43660/05_2025/8vyg_43660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyg_43660/05_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_43660/05_2025/8vyg_43660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyg_43660/05_2025/8vyg_43660.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyg_43660/05_2025/8vyg_43660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyg_43660/05_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-5687/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: 4.52, per 1000 atoms: 1.41 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: 0.73 Conformation dependent library (CDL) restraints added in 391.6 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 13.9% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.540A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.941A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 386 through 389 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.778A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 7.260A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.567A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 120 hydrogen bonds defined for protein. 276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 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: 0.010 Normalize map: mean=0, sd=1: 8.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- 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 : 0.334 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1917 time to fit residues: 23.2843 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 116 ASN B 6 GLN B 90 GLN B 92 HIS R 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140934 restraints weight = 5897.969| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.80 r_work: 0.3739 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 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 : 0.356 Fit side-chains REVERT: A 23 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7001 (tppt) REVERT: A 47 TRP cc_start: 0.7678 (t60) cc_final: 0.7444 (t60) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.2059 time to fit residues: 16.6086 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 : 0.362 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135362 restraints weight = 5830.862| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.59 r_work: 0.3665 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3287 Z= 0.204 Angle : 0.649 6.526 4475 Z= 0.342 Chirality : 0.046 0.140 487 Planarity : 0.006 0.040 577 Dihedral : 5.059 27.826 480 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.18 % Allowed : 13.73 % Favored : 82.09 % 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: 0.37 (0.42), residues: 408 helix: -3.98 (0.71), residues: 26 sheet: 1.19 (0.42), residues: 156 loop : 0.17 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.019 0.002 PHE R 377 TYR 0.018 0.002 TYR A 60 ARG 0.005 0.001 ARG R 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 2.41793 ( 3) hydrogen bonds : bond 0.04180 ( 116) hydrogen bonds : angle 6.34119 ( 276) SS BOND : bond 0.00575 ( 5) SS BOND : angle 1.55012 ( 10) covalent geometry : bond 0.00474 ( 3281) covalent geometry : angle 0.64268 ( 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 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.360 Fit side-chains REVERT: A 23 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7306 (tppt) REVERT: A 47 TRP cc_start: 0.7803 (t60) cc_final: 0.7589 (t60) REVERT: R 444 LYS cc_start: 0.6783 (ptpt) cc_final: 0.6453 (pttp) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.2145 time to fit residues: 16.9085 Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 B residue 91 GLN 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: 3.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.169290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137176 restraints weight = 5930.288| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.58 r_work: 0.3693 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3287 Z= 0.124 Angle : 0.535 5.961 4475 Z= 0.284 Chirality : 0.044 0.140 487 Planarity : 0.005 0.037 577 Dihedral : 4.577 25.749 480 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.41 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: 0.25 (0.42), residues: 408 helix: -3.90 (0.69), residues: 26 sheet: 0.88 (0.41), residues: 169 loop : 0.22 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.011 0.001 PHE B 72 TYR 0.015 0.002 TYR R 380 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.89514 ( 3) hydrogen bonds : bond 0.03424 ( 116) hydrogen bonds : angle 6.05720 ( 276) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.33095 ( 10) covalent geometry : bond 0.00282 ( 3281) covalent geometry : angle 0.53002 ( 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 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.451 Fit side-chains REVERT: A 23 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7376 (tppt) REVERT: A 47 TRP cc_start: 0.7841 (t60) cc_final: 0.7589 (t60) REVERT: R 346 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7440 (mtp85) REVERT: R 444 LYS cc_start: 0.6726 (ptpt) cc_final: 0.6351 (pttp) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.1888 time to fit residues: 13.7427 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 : 0.358 ------------------------------------------------------------------------------- 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 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 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 chunk 33 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 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 = 0.4186 r_free = 0.4186 target = 0.170398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138773 restraints weight = 5802.629| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.53 r_work: 0.3716 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3287 Z= 0.093 Angle : 0.486 5.937 4475 Z= 0.257 Chirality : 0.043 0.139 487 Planarity : 0.004 0.039 577 Dihedral : 4.258 24.885 480 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.09 % Allowed : 16.72 % Favored : 81.19 % 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: 0.24 (0.42), residues: 408 helix: -3.76 (0.72), residues: 26 sheet: 0.89 (0.41), residues: 168 loop : 0.19 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.001 0.000 HIS B 92 PHE 0.010 0.001 PHE B 72 TYR 0.017 0.001 TYR A 54 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 1) link_NAG-ASN : angle 1.58998 ( 3) hydrogen bonds : bond 0.03069 ( 116) hydrogen bonds : angle 5.80790 ( 276) SS BOND : bond 0.00143 ( 5) SS BOND : angle 1.11758 ( 10) covalent geometry : bond 0.00207 ( 3281) covalent geometry : angle 0.48212 ( 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 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.353 Fit side-chains REVERT: A 6 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.5766 (mp10) REVERT: A 23 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7316 (tppt) REVERT: A 36 TRP cc_start: 0.7855 (m100) cc_final: 0.7618 (m100) REVERT: A 47 TRP cc_start: 0.7792 (t60) cc_final: 0.7558 (t60) REVERT: R 346 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7411 (mtp85) REVERT: R 369 TYR cc_start: 0.6286 (t80) cc_final: 0.5819 (t80) REVERT: R 444 LYS cc_start: 0.6695 (ptpt) cc_final: 0.6377 (pttp) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.1867 time to fit residues: 12.0246 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.0030 chunk 7 optimal weight: 0.0570 chunk 39 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4191 r_free = 0.4191 target = 0.170088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138656 restraints weight = 5902.224| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.59 r_work: 0.3710 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5430 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= 0.095 Angle : 0.475 6.440 4475 Z= 0.251 Chirality : 0.043 0.140 487 Planarity : 0.004 0.040 577 Dihedral : 4.087 25.070 480 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.69 % Allowed : 16.12 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.43), residues: 408 helix: -3.66 (0.72), residues: 26 sheet: 0.88 (0.41), residues: 168 loop : 0.24 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.010 0.001 PHE B 72 TYR 0.015 0.001 TYR A 54 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 1.56507 ( 3) hydrogen bonds : bond 0.02962 ( 116) hydrogen bonds : angle 5.73149 ( 276) SS BOND : bond 0.00118 ( 5) SS BOND : angle 0.96046 ( 10) covalent geometry : bond 0.00214 ( 3281) covalent geometry : angle 0.47150 ( 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 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.353 Fit side-chains REVERT: A 23 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7219 (tppt) REVERT: A 47 TRP cc_start: 0.7769 (t60) cc_final: 0.7497 (t60) REVERT: R 346 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.7444 (mtp85) REVERT: R 369 TYR cc_start: 0.6319 (t80) cc_final: 0.5911 (t80) REVERT: R 444 LYS cc_start: 0.6708 (ptpt) cc_final: 0.6407 (pttp) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.1880 time to fit residues: 11.6794 Evaluate side-chains 52 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain 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: 1.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 36 optimal weight: 0.0570 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.170020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138768 restraints weight = 5891.442| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.50 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: 0.7580 moved from start: 0.5544 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 : 0.488 6.524 4475 Z= 0.256 Chirality : 0.043 0.140 487 Planarity : 0.004 0.042 577 Dihedral : 4.128 24.772 480 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.58 % Allowed : 15.22 % Favored : 81.19 % 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: 0.37 (0.43), residues: 408 helix: -3.64 (0.74), residues: 26 sheet: 0.97 (0.41), residues: 168 loop : 0.27 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.013 0.001 PHE B 72 TYR 0.015 0.001 TYR R 380 ARG 0.001 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 1.62765 ( 3) hydrogen bonds : bond 0.03066 ( 116) hydrogen bonds : angle 5.88322 ( 276) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.83989 ( 10) covalent geometry : bond 0.00242 ( 3281) covalent geometry : angle 0.48558 ( 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 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.330 Fit side-chains REVERT: A 23 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7364 (tppt) REVERT: A 47 TRP cc_start: 0.7738 (t60) cc_final: 0.7404 (t60) REVERT: R 369 TYR cc_start: 0.6320 (t80) cc_final: 0.5909 (t80) REVERT: R 444 LYS cc_start: 0.6800 (ptpt) cc_final: 0.6397 (pttp) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.1703 time to fit residues: 11.5056 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 overall best weight: 0.2830 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4198 r_free = 0.4198 target = 0.170911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140387 restraints weight = 5873.727| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.55 r_work: 0.3734 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5606 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= 0.085 Angle : 0.489 9.032 4475 Z= 0.252 Chirality : 0.043 0.138 487 Planarity : 0.004 0.043 577 Dihedral : 3.954 23.598 480 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 (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: 0.47 (0.43), residues: 408 helix: -3.59 (0.73), residues: 26 sheet: 1.07 (0.41), residues: 168 loop : 0.31 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.001 0.001 HIS B 92 PHE 0.009 0.001 PHE B 72 TYR 0.020 0.001 TYR A 54 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.45106 ( 3) hydrogen bonds : bond 0.02867 ( 116) hydrogen bonds : angle 5.77464 ( 276) SS BOND : bond 0.00177 ( 5) SS BOND : angle 0.70260 ( 10) covalent geometry : bond 0.00184 ( 3281) covalent geometry : angle 0.48674 ( 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 : 0.353 Fit side-chains REVERT: A 23 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7264 (tppt) REVERT: A 36 TRP cc_start: 0.7859 (m100) cc_final: 0.7628 (m100) REVERT: A 47 TRP cc_start: 0.7755 (t60) cc_final: 0.7454 (t60) REVERT: B 90 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6706 (tm-30) REVERT: R 369 TYR cc_start: 0.6233 (t80) cc_final: 0.5818 (t80) outliers start: 8 outliers final: 8 residues processed: 53 average time/residue: 0.1842 time to fit residues: 11.7322 Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP 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: 5.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139703 restraints weight = 5894.607| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.47 r_work: 0.3732 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3287 Z= 0.102 Angle : 0.505 8.847 4475 Z= 0.259 Chirality : 0.043 0.139 487 Planarity : 0.004 0.044 577 Dihedral : 4.109 24.675 480 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.58 % Allowed : 16.72 % 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: 0.47 (0.43), residues: 408 helix: -3.57 (0.74), residues: 26 sheet: 1.07 (0.41), residues: 168 loop : 0.31 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.001 0.000 HIS B 92 PHE 0.012 0.001 PHE B 72 TYR 0.020 0.002 TYR A 54 ARG 0.001 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 1.55104 ( 3) hydrogen bonds : bond 0.03012 ( 116) hydrogen bonds : angle 5.86710 ( 276) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.74889 ( 10) covalent geometry : bond 0.00230 ( 3281) covalent geometry : angle 0.50275 ( 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 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.375 Fit side-chains REVERT: A 23 LYS cc_start: 0.7815 (ttmm) cc_final: 0.7295 (tppt) REVERT: A 47 TRP cc_start: 0.7749 (t60) cc_final: 0.7426 (t60) REVERT: R 369 TYR cc_start: 0.6258 (t80) cc_final: 0.5839 (t80) outliers start: 12 outliers final: 12 residues processed: 56 average time/residue: 0.1745 time to fit residues: 11.8299 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 448 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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** R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140431 restraints weight = 5873.612| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.50 r_work: 0.3743 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5818 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= 0.091 Angle : 0.513 9.870 4475 Z= 0.262 Chirality : 0.043 0.139 487 Planarity : 0.004 0.044 577 Dihedral : 4.021 24.409 480 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.28 % Allowed : 16.72 % 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: 0.52 (0.43), residues: 408 helix: -3.55 (0.74), residues: 26 sheet: 1.08 (0.41), residues: 170 loop : 0.37 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 36 HIS 0.000 0.000 HIS B 92 PHE 0.016 0.001 PHE B 98 TYR 0.019 0.002 TYR A 54 ARG 0.007 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 1.47543 ( 3) hydrogen bonds : bond 0.02943 ( 116) hydrogen bonds : angle 5.79380 ( 276) SS BOND : bond 0.00214 ( 5) SS BOND : angle 0.74137 ( 10) covalent geometry : bond 0.00201 ( 3281) covalent geometry : angle 0.51101 ( 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 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.338 Fit side-chains REVERT: A 23 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7273 (tppt) REVERT: A 47 TRP cc_start: 0.7728 (t60) cc_final: 0.7417 (t60) REVERT: R 369 TYR cc_start: 0.6228 (t80) cc_final: 0.5816 (t80) REVERT: R 444 LYS cc_start: 0.6521 (pttm) cc_final: 0.5573 (mmmt) outliers start: 11 outliers final: 10 residues processed: 54 average time/residue: 0.1871 time to fit residues: 12.0490 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 448 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN 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 = 0.169292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138353 restraints weight = 5821.513| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.46 r_work: 0.3716 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5896 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= 0.133 Angle : 0.558 9.633 4475 Z= 0.284 Chirality : 0.044 0.138 487 Planarity : 0.005 0.044 577 Dihedral : 4.326 26.449 480 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 0.45 (0.43), residues: 408 helix: -3.55 (0.76), residues: 26 sheet: 1.15 (0.41), residues: 167 loop : 0.20 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 36 HIS 0.001 0.001 HIS B 92 PHE 0.015 0.001 PHE B 72 TYR 0.019 0.002 TYR A 54 ARG 0.006 0.000 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.79261 ( 3) hydrogen bonds : bond 0.03279 ( 116) hydrogen bonds : angle 6.00225 ( 276) SS BOND : bond 0.00312 ( 5) SS BOND : angle 0.86371 ( 10) covalent geometry : bond 0.00307 ( 3281) covalent geometry : angle 0.55577 ( 4462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.53 seconds wall clock time: 44 minutes 1.97 seconds (2641.97 seconds total)