Starting phenix.real_space_refine on Wed Jul 23 12:57:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khd_37241/07_2025/8khd_37241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khd_37241/07_2025/8khd_37241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8khd_37241/07_2025/8khd_37241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khd_37241/07_2025/8khd_37241.map" model { file = "/net/cci-nas-00/data/ceres_data/8khd_37241/07_2025/8khd_37241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khd_37241/07_2025/8khd_37241.cif" } resolution = 3.5 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= -0.002 sd= 0.057 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 17 5.16 5 C 2112 2.51 5 N 561 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3337 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 917 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1600 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.98 Number of scatterers: 3337 At special positions: 0 Unit cell: (69.96, 90.1, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 647 8.00 N 561 7.00 C 2112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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 C 601 " - " ASN C 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 373.1 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 3.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.696A pdb=" N ASP H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 408 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.501A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 106 removed outlier: 4.357A pdb=" N VAL H 105 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 466 " --> pdb=" O VAL H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.699A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.600A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 85 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1087 1.35 - 1.48: 932 1.48 - 1.61: 1377 1.61 - 1.74: 0 1.74 - 1.87: 22 Bond restraints: 3418 Sorted by residual: bond pdb=" CG1 ILE C 434 " pdb=" CD1 ILE C 434 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.67e+00 bond pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 1.808 1.865 -0.057 3.30e-02 9.18e+02 3.00e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" CA ASN C 331 " pdb=" C ASN C 331 " ideal model delta sigma weight residual 1.521 1.537 -0.016 9.90e-03 1.02e+04 2.67e+00 bond pdb=" C ASN C 331 " pdb=" N ILE C 332 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.18e+00 ... (remaining 3413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 4514 2.33 - 4.66: 113 4.66 - 6.99: 18 6.99 - 9.32: 4 9.32 - 11.65: 1 Bond angle restraints: 4650 Sorted by residual: angle pdb=" C ASN C 331 " pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 121.70 129.97 -8.27 1.80e+00 3.09e-01 2.11e+01 angle pdb=" C VAL J 97 " pdb=" N ILE J 98 " pdb=" CA ILE J 98 " ideal model delta sigma weight residual 121.97 129.47 -7.50 1.80e+00 3.09e-01 1.73e+01 angle pdb=" CB MET H 122 " pdb=" CG MET H 122 " pdb=" SD MET H 122 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 114.40 123.01 -8.61 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA TYR H 109 " pdb=" CB TYR H 109 " pdb=" CG TYR H 109 " ideal model delta sigma weight residual 113.90 120.63 -6.73 1.80e+00 3.09e-01 1.40e+01 ... (remaining 4645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1834 17.62 - 35.25: 158 35.25 - 52.87: 23 52.87 - 70.49: 5 70.49 - 88.11: 2 Dihedral angle restraints: 2022 sinusoidal: 781 harmonic: 1241 Sorted by residual: dihedral pdb=" CA ALA C 372 " pdb=" C ALA C 372 " pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA CYS C 379 " pdb=" C CYS C 379 " pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 58.41 34.59 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 355 0.045 - 0.089: 103 0.089 - 0.134: 47 0.134 - 0.178: 1 0.178 - 0.223: 3 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR H 59 " pdb=" CA THR H 59 " pdb=" OG1 THR H 59 " pdb=" CG2 THR H 59 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA CYS C 379 " pdb=" N CYS C 379 " pdb=" C CYS C 379 " pdb=" CB CYS C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 506 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 374 " 0.015 2.00e-02 2.50e+03 1.66e-02 4.82e+00 pdb=" CG PHE C 374 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 374 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 374 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 374 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 374 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 374 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 108 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C MET H 108 " 0.037 2.00e-02 2.50e+03 pdb=" O MET H 108 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR H 109 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J 7 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO J 8 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO J 8 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 8 " 0.028 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 952 2.81 - 3.33: 2787 3.33 - 3.85: 5267 3.85 - 4.38: 5755 4.38 - 4.90: 10283 Nonbonded interactions: 25044 Sorted by model distance: nonbonded pdb=" OG SER J 64 " pdb=" OG SER J 71 " model vdw 2.287 3.040 nonbonded pdb=" OG SER J 66 " pdb=" OG1 THR J 69 " model vdw 2.302 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.313 3.040 nonbonded pdb=" O VAL J 97 " pdb=" N PHE J 99 " model vdw 2.354 3.120 nonbonded pdb=" O ILE H 55 " pdb=" ND2 ASN C 354 " model vdw 2.355 3.120 ... (remaining 25039 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 group one per residue 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: 3.340 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 : 0.004 0.075 3425 Z= 0.189 Angle : 0.884 11.654 4665 Z= 0.467 Chirality : 0.050 0.223 509 Planarity : 0.006 0.051 604 Dihedral : 13.417 88.113 1218 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.39 (0.41), residues: 426 helix: -4.55 (0.52), residues: 13 sheet: 0.98 (0.49), residues: 122 loop : -1.74 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 353 HIS 0.002 0.001 HIS J 96 PHE 0.039 0.002 PHE C 374 TYR 0.034 0.002 TYR C 369 ARG 0.006 0.001 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 1) link_NAG-ASN : angle 2.26007 ( 3) hydrogen bonds : bond 0.10069 ( 85) hydrogen bonds : angle 7.87130 ( 219) SS BOND : bond 0.01016 ( 6) SS BOND : angle 2.23600 ( 12) covalent geometry : bond 0.00405 ( 3418) covalent geometry : angle 0.87647 ( 4650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2134 time to fit residues: 19.9623 Evaluate side-chains 64 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN C 394 ASN C 474 GLN ** C 506 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 = 0.151079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120578 restraints weight = 6115.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.125135 restraints weight = 3583.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128235 restraints weight = 2564.226| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3425 Z= 0.142 Angle : 0.630 7.937 4665 Z= 0.329 Chirality : 0.043 0.174 509 Planarity : 0.005 0.043 604 Dihedral : 5.568 29.497 496 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.51 % Favored : 92.25 % Rotamer: Outliers : 2.80 % Allowed : 10.64 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.26 (0.41), residues: 426 helix: -4.32 (0.67), residues: 19 sheet: 1.23 (0.49), residues: 121 loop : -1.65 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 PHE 0.010 0.001 PHE C 400 TYR 0.012 0.001 TYR J 48 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 1) link_NAG-ASN : angle 2.21960 ( 3) hydrogen bonds : bond 0.03394 ( 85) hydrogen bonds : angle 5.97015 ( 219) SS BOND : bond 0.00608 ( 6) SS BOND : angle 1.63648 ( 12) covalent geometry : bond 0.00325 ( 3418) covalent geometry : angle 0.62306 ( 4650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6388 (ptp) REVERT: J 48 TYR cc_start: 0.7325 (p90) cc_final: 0.7104 (p90) REVERT: J 69 THR cc_start: 0.8504 (p) cc_final: 0.8171 (p) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.1491 time to fit residues: 13.6733 Evaluate side-chains 66 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.150838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121690 restraints weight = 6018.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126011 restraints weight = 3595.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.129085 restraints weight = 2595.387| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3425 Z= 0.115 Angle : 0.598 8.035 4665 Z= 0.307 Chirality : 0.043 0.168 509 Planarity : 0.004 0.040 604 Dihedral : 5.104 26.339 496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.98 % Favored : 91.78 % Rotamer: Outliers : 2.24 % Allowed : 16.25 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.02 (0.41), residues: 426 helix: -3.72 (1.16), residues: 13 sheet: 1.38 (0.48), residues: 119 loop : -1.55 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE C 338 TYR 0.013 0.001 TYR C 380 ARG 0.002 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 1) link_NAG-ASN : angle 1.95053 ( 3) hydrogen bonds : bond 0.02981 ( 85) hydrogen bonds : angle 5.55489 ( 219) SS BOND : bond 0.00632 ( 6) SS BOND : angle 1.38376 ( 12) covalent geometry : bond 0.00262 ( 3418) covalent geometry : angle 0.59305 ( 4650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 92 ASP cc_start: 0.7923 (m-30) cc_final: 0.7712 (m-30) REVERT: H 107 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6148 (ptp) REVERT: J 48 TYR cc_start: 0.7288 (p90) cc_final: 0.7022 (p90) REVERT: J 69 THR cc_start: 0.8466 (p) cc_final: 0.8140 (p) REVERT: C 390 LEU cc_start: 0.7284 (pt) cc_final: 0.6822 (tt) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.2206 time to fit residues: 21.0595 Evaluate side-chains 71 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 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 = 0.4231 r_free = 0.4231 target = 0.155095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123005 restraints weight = 6446.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.127743 restraints weight = 3519.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.130813 restraints weight = 2495.529| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3425 Z= 0.123 Angle : 0.599 8.205 4665 Z= 0.307 Chirality : 0.043 0.166 509 Planarity : 0.004 0.039 604 Dihedral : 5.062 25.180 496 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 2.80 % Allowed : 17.93 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.12 (0.41), residues: 426 helix: -3.86 (0.87), residues: 19 sheet: 1.33 (0.48), residues: 119 loop : -1.56 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.016 0.001 PHE C 338 TYR 0.010 0.001 TYR C 380 ARG 0.002 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 1) link_NAG-ASN : angle 2.13216 ( 3) hydrogen bonds : bond 0.03033 ( 85) hydrogen bonds : angle 5.35309 ( 219) SS BOND : bond 0.00725 ( 6) SS BOND : angle 1.76484 ( 12) covalent geometry : bond 0.00282 ( 3418) covalent geometry : angle 0.59073 ( 4650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 69 THR cc_start: 0.8518 (p) cc_final: 0.8189 (p) REVERT: C 357 ARG cc_start: 0.7800 (tpt-90) cc_final: 0.7574 (tpt-90) REVERT: C 360 ASN cc_start: 0.8764 (m110) cc_final: 0.8498 (m-40) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.2770 time to fit residues: 26.3821 Evaluate side-chains 70 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.150477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.121383 restraints weight = 6093.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.125709 restraints weight = 3620.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128559 restraints weight = 2620.403| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3425 Z= 0.113 Angle : 0.600 8.294 4665 Z= 0.312 Chirality : 0.043 0.164 509 Planarity : 0.004 0.037 604 Dihedral : 5.018 23.486 496 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 3.08 % Allowed : 18.77 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.10 (0.42), residues: 426 helix: -4.00 (0.70), residues: 19 sheet: 1.17 (0.48), residues: 124 loop : -1.49 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE C 338 TYR 0.011 0.001 TYR H 97 ARG 0.002 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 1) link_NAG-ASN : angle 2.10789 ( 3) hydrogen bonds : bond 0.02853 ( 85) hydrogen bonds : angle 5.20528 ( 219) SS BOND : bond 0.00556 ( 6) SS BOND : angle 1.66640 ( 12) covalent geometry : bond 0.00254 ( 3418) covalent geometry : angle 0.59238 ( 4650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 92 ASP cc_start: 0.8018 (m-30) cc_final: 0.7694 (m-30) REVERT: J 69 THR cc_start: 0.8497 (p) cc_final: 0.8183 (p) REVERT: C 360 ASN cc_start: 0.8684 (m110) cc_final: 0.8418 (m-40) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 0.1881 time to fit residues: 18.4925 Evaluate side-chains 69 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.0020 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 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 = 0.4179 r_free = 0.4179 target = 0.151591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122312 restraints weight = 6177.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126858 restraints weight = 3542.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129910 restraints weight = 2512.855| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3425 Z= 0.107 Angle : 0.589 8.700 4665 Z= 0.302 Chirality : 0.043 0.163 509 Planarity : 0.004 0.037 604 Dihedral : 4.902 22.124 496 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 1.96 % Allowed : 19.33 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.00 (0.42), residues: 426 helix: -3.90 (0.66), residues: 19 sheet: 1.24 (0.48), residues: 123 loop : -1.41 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.010 0.001 PHE C 374 TYR 0.012 0.001 TYR C 380 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 1) link_NAG-ASN : angle 2.15658 ( 3) hydrogen bonds : bond 0.02696 ( 85) hydrogen bonds : angle 5.14517 ( 219) SS BOND : bond 0.00626 ( 6) SS BOND : angle 1.82003 ( 12) covalent geometry : bond 0.00241 ( 3418) covalent geometry : angle 0.58014 ( 4650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: J 69 THR cc_start: 0.8458 (p) cc_final: 0.8220 (p) REVERT: C 360 ASN cc_start: 0.8587 (m110) cc_final: 0.8343 (m-40) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.1609 time to fit residues: 15.1382 Evaluate side-chains 70 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 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 = 0.4251 r_free = 0.4251 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.124842 restraints weight = 6367.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.129660 restraints weight = 3448.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.132866 restraints weight = 2422.741| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3425 Z= 0.109 Angle : 0.605 8.207 4665 Z= 0.311 Chirality : 0.043 0.161 509 Planarity : 0.004 0.037 604 Dihedral : 4.841 20.924 496 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.04 % Favored : 92.72 % Rotamer: Outliers : 2.52 % Allowed : 18.77 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.96 (0.42), residues: 426 helix: -3.78 (0.69), residues: 19 sheet: 1.27 (0.48), residues: 123 loop : -1.39 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE C 338 TYR 0.014 0.001 TYR J 48 ARG 0.002 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 1) link_NAG-ASN : angle 2.06696 ( 3) hydrogen bonds : bond 0.02709 ( 85) hydrogen bonds : angle 5.11381 ( 219) SS BOND : bond 0.00564 ( 6) SS BOND : angle 1.62924 ( 12) covalent geometry : bond 0.00250 ( 3418) covalent geometry : angle 0.59751 ( 4650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: J 48 TYR cc_start: 0.7057 (p90) cc_final: 0.6503 (p90) REVERT: J 69 THR cc_start: 0.8466 (p) cc_final: 0.8206 (p) REVERT: C 360 ASN cc_start: 0.8750 (m110) cc_final: 0.8456 (m110) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.2690 time to fit residues: 25.4198 Evaluate side-chains 68 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 GLN ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.155010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121187 restraints weight = 6536.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.126018 restraints weight = 3559.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.129148 restraints weight = 2525.704| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3425 Z= 0.147 Angle : 0.638 8.001 4665 Z= 0.336 Chirality : 0.044 0.163 509 Planarity : 0.005 0.038 604 Dihedral : 5.143 21.906 496 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 2.80 % Allowed : 19.05 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.96 (0.42), residues: 426 helix: -3.60 (0.80), residues: 19 sheet: 1.23 (0.48), residues: 122 loop : -1.37 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE C 400 TYR 0.010 0.001 TYR H 109 ARG 0.004 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 1) link_NAG-ASN : angle 2.23630 ( 3) hydrogen bonds : bond 0.03156 ( 85) hydrogen bonds : angle 5.27600 ( 219) SS BOND : bond 0.00646 ( 6) SS BOND : angle 1.79053 ( 12) covalent geometry : bond 0.00338 ( 3418) covalent geometry : angle 0.62999 ( 4650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.8143 (m-30) cc_final: 0.7933 (m-30) REVERT: J 69 THR cc_start: 0.8622 (p) cc_final: 0.8387 (p) REVERT: J 104 LYS cc_start: 0.7019 (ttmm) cc_final: 0.6131 (tmtt) REVERT: C 360 ASN cc_start: 0.8832 (m110) cc_final: 0.8553 (m110) REVERT: C 390 LEU cc_start: 0.7391 (pt) cc_final: 0.6981 (tt) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.1629 time to fit residues: 14.0886 Evaluate side-chains 72 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.120385 restraints weight = 6536.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.125272 restraints weight = 3588.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.128401 restraints weight = 2530.880| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3425 Z= 0.154 Angle : 0.653 8.890 4665 Z= 0.339 Chirality : 0.044 0.165 509 Planarity : 0.005 0.047 604 Dihedral : 5.252 21.901 496 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.61 % Rotamer: Outliers : 3.08 % Allowed : 19.61 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.01 (0.42), residues: 426 helix: -3.53 (0.84), residues: 19 sheet: 1.09 (0.47), residues: 122 loop : -1.36 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS J 96 PHE 0.008 0.001 PHE C 400 TYR 0.010 0.001 TYR C 380 ARG 0.004 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 1) link_NAG-ASN : angle 2.33286 ( 3) hydrogen bonds : bond 0.03241 ( 85) hydrogen bonds : angle 5.42023 ( 219) SS BOND : bond 0.00623 ( 6) SS BOND : angle 1.67664 ( 12) covalent geometry : bond 0.00355 ( 3418) covalent geometry : angle 0.64529 ( 4650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.8147 (m-30) cc_final: 0.7926 (m-30) REVERT: J 69 THR cc_start: 0.8658 (p) cc_final: 0.8419 (p) REVERT: J 104 LYS cc_start: 0.6973 (ttmm) cc_final: 0.6066 (tmtt) REVERT: C 360 ASN cc_start: 0.8884 (m110) cc_final: 0.8604 (m110) outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.1520 time to fit residues: 14.3139 Evaluate side-chains 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** 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 = 0.4202 r_free = 0.4202 target = 0.152987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.120858 restraints weight = 6462.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.125684 restraints weight = 3537.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.128843 restraints weight = 2493.256| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3425 Z= 0.144 Angle : 0.661 8.799 4665 Z= 0.343 Chirality : 0.044 0.164 509 Planarity : 0.005 0.042 604 Dihedral : 5.199 20.919 496 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.61 % Rotamer: Outliers : 2.52 % Allowed : 21.01 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.03 (0.42), residues: 426 helix: -3.44 (0.87), residues: 18 sheet: 0.79 (0.46), residues: 130 loop : -1.30 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE H 82 TYR 0.012 0.001 TYR J 48 ARG 0.003 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 1) link_NAG-ASN : angle 2.31433 ( 3) hydrogen bonds : bond 0.03113 ( 85) hydrogen bonds : angle 5.38626 ( 219) SS BOND : bond 0.00635 ( 6) SS BOND : angle 1.71922 ( 12) covalent geometry : bond 0.00330 ( 3418) covalent geometry : angle 0.65350 ( 4650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.8150 (m-30) cc_final: 0.7946 (m-30) REVERT: J 48 TYR cc_start: 0.7336 (p90) cc_final: 0.6639 (p90) REVERT: J 69 THR cc_start: 0.8636 (p) cc_final: 0.8394 (p) REVERT: J 104 LYS cc_start: 0.6976 (ttmm) cc_final: 0.6079 (tmtt) REVERT: C 360 ASN cc_start: 0.8871 (m110) cc_final: 0.8607 (m110) outliers start: 9 outliers final: 9 residues processed: 73 average time/residue: 0.1601 time to fit residues: 14.2876 Evaluate side-chains 75 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** 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 = 0.4233 r_free = 0.4233 target = 0.155361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.122689 restraints weight = 6641.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.127593 restraints weight = 3596.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.130806 restraints weight = 2544.853| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3425 Z= 0.129 Angle : 0.658 8.768 4665 Z= 0.340 Chirality : 0.044 0.164 509 Planarity : 0.005 0.057 604 Dihedral : 5.073 19.601 496 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 2.52 % Allowed : 20.73 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.98 (0.43), residues: 426 helix: -3.43 (0.89), residues: 18 sheet: 0.98 (0.47), residues: 121 loop : -1.27 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.011 0.001 PHE H 82 TYR 0.013 0.001 TYR J 48 ARG 0.003 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 1) link_NAG-ASN : angle 2.24376 ( 3) hydrogen bonds : bond 0.03048 ( 85) hydrogen bonds : angle 5.37603 ( 219) SS BOND : bond 0.00592 ( 6) SS BOND : angle 1.60397 ( 12) covalent geometry : bond 0.00293 ( 3418) covalent geometry : angle 0.65174 ( 4650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.86 seconds wall clock time: 42 minutes 15.59 seconds (2535.59 seconds total)