Starting phenix.real_space_refine on Tue Feb 11 00:12:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khd_37241/02_2025/8khd_37241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khd_37241/02_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_37241/02_2025/8khd_37241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khd_37241/02_2025/8khd_37241.map" model { file = "/net/cci-nas-00/data/ceres_data/8khd_37241/02_2025/8khd_37241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khd_37241/02_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-5592/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: 3.44, per 1000 atoms: 1.03 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: 0.75 Conformation dependent library (CDL) restraints added in 437.8 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: 0.38 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: 0.84 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.560 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- 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 3418 Z= 0.271 Angle : 0.876 11.654 4650 Z= 0.464 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 *********************** 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 : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1894 time to fit residues: 17.9894 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 : 0.424 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.154117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.120896 restraints weight = 6478.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.125526 restraints weight = 3557.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.128809 restraints weight = 2538.820| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3418 Z= 0.273 Angle : 0.657 7.968 4650 Z= 0.345 Chirality : 0.044 0.182 509 Planarity : 0.005 0.041 604 Dihedral : 5.749 30.123 496 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 3.36 % Allowed : 11.76 % Favored : 84.87 % 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: -1.30 (0.41), residues: 426 helix: -4.36 (0.66), residues: 19 sheet: 1.13 (0.48), residues: 123 loop : -1.66 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 PHE 0.012 0.001 PHE C 400 TYR 0.012 0.002 TYR C 369 ARG 0.003 0.001 ARG C 509 *********************** 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 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.432 Fit side-chains REVERT: H 107 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6529 (ptp) REVERT: J 48 TYR cc_start: 0.7491 (p90) cc_final: 0.7232 (p90) REVERT: C 360 ASN cc_start: 0.8694 (m-40) cc_final: 0.8404 (m-40) REVERT: C 390 LEU cc_start: 0.7528 (pt) cc_final: 0.7091 (tt) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.1498 time to fit residues: 13.3058 Evaluate side-chains 65 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 402 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.153272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.121199 restraints weight = 6326.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.125815 restraints weight = 3514.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128868 restraints weight = 2490.639| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3418 Z= 0.255 Angle : 0.640 8.224 4650 Z= 0.332 Chirality : 0.044 0.172 509 Planarity : 0.005 0.040 604 Dihedral : 5.559 28.676 496 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.69 % Favored : 91.08 % Rotamer: Outliers : 2.80 % Allowed : 17.37 % Favored : 79.83 % 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: -1.13 (0.41), residues: 426 helix: -3.61 (1.16), residues: 12 sheet: 1.18 (0.49), residues: 119 loop : -1.59 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.009 0.001 PHE C 400 TYR 0.013 0.002 TYR C 380 ARG 0.003 0.000 ARG C 509 *********************** 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 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: J 68 ASN cc_start: 0.8309 (p0) cc_final: 0.8071 (p0) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1347 time to fit residues: 12.6382 Evaluate side-chains 72 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 402 ILE 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: 0.7980 chunk 41 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.151357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.122597 restraints weight = 6173.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.127176 restraints weight = 3432.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.130247 restraints weight = 2414.598| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3418 Z= 0.158 Angle : 0.594 8.008 4650 Z= 0.306 Chirality : 0.043 0.166 509 Planarity : 0.004 0.039 604 Dihedral : 5.071 25.938 496 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 1.96 % Allowed : 19.61 % Favored : 78.43 % 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: -1.17 (0.42), residues: 426 helix: -4.01 (0.82), residues: 19 sheet: 1.19 (0.49), residues: 122 loop : -1.56 (0.37), residues: 285 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 0.016 0.001 TYR C 369 ARG 0.002 0.000 ARG C 454 *********************** 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 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: J 48 TYR cc_start: 0.7461 (p90) cc_final: 0.7214 (p90) REVERT: J 68 ASN cc_start: 0.8284 (p0) cc_final: 0.8067 (p0) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.1303 time to fit residues: 12.5903 Evaluate side-chains 66 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 433 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: 0.0970 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.149599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.126958 restraints weight = 6166.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.129678 restraints weight = 3761.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.131931 restraints weight = 2973.803| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3418 Z= 0.184 Angle : 0.608 8.454 4650 Z= 0.314 Chirality : 0.043 0.164 509 Planarity : 0.004 0.037 604 Dihedral : 5.151 25.008 496 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.61 % Rotamer: Outliers : 4.20 % Allowed : 16.81 % Favored : 78.99 % 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: -1.13 (0.42), residues: 426 helix: -3.97 (0.80), residues: 19 sheet: 1.09 (0.48), residues: 125 loop : -1.49 (0.38), residues: 282 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 0.016 0.001 PHE C 338 TYR 0.012 0.001 TYR H 109 ARG 0.004 0.001 ARG C 357 *********************** 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 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.7975 (m-30) cc_final: 0.7718 (m-30) REVERT: J 48 TYR cc_start: 0.7423 (p90) cc_final: 0.7216 (p90) REVERT: J 68 ASN cc_start: 0.8274 (p0) cc_final: 0.7964 (p0) REVERT: C 390 LEU cc_start: 0.7347 (pt) cc_final: 0.6851 (tt) REVERT: C 406 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6938 (mp0) outliers start: 15 outliers final: 10 residues processed: 80 average time/residue: 0.1244 time to fit residues: 12.6923 Evaluate side-chains 76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 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: 0.7980 chunk 32 optimal weight: 0.0470 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.155363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.123523 restraints weight = 6564.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.128538 restraints weight = 3512.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.131753 restraints weight = 2431.799| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3418 Z= 0.177 Angle : 0.602 7.591 4650 Z= 0.313 Chirality : 0.044 0.160 509 Planarity : 0.004 0.037 604 Dihedral : 5.014 23.702 496 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.31 % Rotamer: Outliers : 2.80 % Allowed : 19.61 % Favored : 77.59 % 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: -1.06 (0.42), residues: 426 helix: -3.85 (0.82), residues: 19 sheet: 1.06 (0.48), residues: 125 loop : -1.40 (0.39), residues: 282 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 0.011 0.001 PHE C 338 TYR 0.012 0.001 TYR C 380 ARG 0.003 0.000 ARG C 357 *********************** 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 77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: H 119 GLN cc_start: 0.7490 (pp30) cc_final: 0.7248 (pp30) REVERT: J 68 ASN cc_start: 0.8325 (p0) cc_final: 0.8086 (p0) REVERT: C 390 LEU cc_start: 0.7385 (pt) cc_final: 0.6984 (tt) REVERT: C 406 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6866 (mp0) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1357 time to fit residues: 12.6720 Evaluate side-chains 73 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 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: 1.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1002 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.147857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118849 restraints weight = 6186.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.123487 restraints weight = 3413.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.126579 restraints weight = 2407.321| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3418 Z= 0.216 Angle : 0.623 9.002 4650 Z= 0.322 Chirality : 0.044 0.162 509 Planarity : 0.004 0.037 604 Dihedral : 5.184 24.114 496 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.69 % Favored : 91.08 % Rotamer: Outliers : 5.04 % Allowed : 17.37 % Favored : 77.59 % 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: -0.99 (0.42), residues: 426 helix: -3.59 (0.90), residues: 19 sheet: 1.30 (0.48), residues: 119 loop : -1.42 (0.38), 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 0.006 0.001 PHE C 400 TYR 0.011 0.001 TYR C 380 ARG 0.002 0.000 ARG C 357 *********************** 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 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: H 119 GLN cc_start: 0.7461 (pp30) cc_final: 0.7193 (pp30) REVERT: J 68 ASN cc_start: 0.8357 (p0) cc_final: 0.8157 (p0) REVERT: J 104 LYS cc_start: 0.6990 (ttmm) cc_final: 0.6104 (tmtt) REVERT: C 357 ARG cc_start: 0.7952 (tmm-80) cc_final: 0.7525 (ttm-80) REVERT: C 406 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6854 (mp0) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.1515 time to fit residues: 15.4885 Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 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: 0.8980 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 422 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.152226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119528 restraints weight = 6539.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.124147 restraints weight = 3576.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127360 restraints weight = 2540.271| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3418 Z= 0.251 Angle : 0.657 8.490 4650 Z= 0.342 Chirality : 0.045 0.161 509 Planarity : 0.005 0.038 604 Dihedral : 5.412 25.148 496 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.61 % Rotamer: Outliers : 5.04 % Allowed : 19.33 % Favored : 75.63 % 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: -1.15 (0.42), residues: 426 helix: -3.56 (0.90), residues: 19 sheet: 1.09 (0.48), residues: 118 loop : -1.48 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS J 96 PHE 0.008 0.001 PHE C 400 TYR 0.011 0.001 TYR H 109 ARG 0.003 0.001 ARG J 19 *********************** 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 88 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 119 GLN cc_start: 0.7368 (pp30) cc_final: 0.7133 (pp30) REVERT: J 68 ASN cc_start: 0.8346 (p0) cc_final: 0.8098 (p0) REVERT: J 104 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6067 (tmtt) REVERT: C 357 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7523 (ttm-80) REVERT: C 406 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6896 (mp0) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.1662 time to fit residues: 16.3465 Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 394 ASN ** C 422 ASN ** 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 = 0.4203 r_free = 0.4203 target = 0.148616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.119607 restraints weight = 6337.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.124322 restraints weight = 3487.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.127416 restraints weight = 2459.708| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3418 Z= 0.215 Angle : 0.663 10.523 4650 Z= 0.338 Chirality : 0.044 0.163 509 Planarity : 0.005 0.047 604 Dihedral : 5.245 24.337 496 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.61 % Rotamer: Outliers : 4.48 % Allowed : 20.17 % Favored : 75.35 % 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: -1.20 (0.42), residues: 426 helix: -3.32 (0.98), residues: 18 sheet: 0.62 (0.45), residues: 130 loop : -1.41 (0.40), residues: 278 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 400 TYR 0.011 0.001 TYR C 380 ARG 0.003 0.000 ARG J 19 *********************** 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 86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 109 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6953 (t80) REVERT: H 119 GLN cc_start: 0.7385 (pp30) cc_final: 0.7165 (pp30) REVERT: J 68 ASN cc_start: 0.8317 (p0) cc_final: 0.8099 (p0) REVERT: J 104 LYS cc_start: 0.7017 (ttmm) cc_final: 0.6136 (tmtt) REVERT: C 357 ARG cc_start: 0.7962 (tmm-80) cc_final: 0.7648 (ttm-80) REVERT: C 406 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6731 (mp0) outliers start: 16 outliers final: 14 residues processed: 79 average time/residue: 0.1583 time to fit residues: 15.2541 Evaluate side-chains 86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 chunk 30 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 overall best weight: 0.5032 ------------------------------------------------------------------------------- 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 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.151395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.122753 restraints weight = 6300.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.127385 restraints weight = 3434.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.130654 restraints weight = 2401.845| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3418 Z= 0.167 Angle : 0.635 9.876 4650 Z= 0.323 Chirality : 0.043 0.158 509 Planarity : 0.004 0.038 604 Dihedral : 4.827 21.575 496 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.81 % Favored : 92.96 % Rotamer: Outliers : 3.64 % Allowed : 21.57 % Favored : 74.79 % 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: -2.30 (1.47), residues: 12 sheet: 0.72 (0.45), residues: 130 loop : -1.30 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 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 ********************** 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 88 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 48 TYR cc_start: 0.7261 (p90) cc_final: 0.6810 (p90) REVERT: J 68 ASN cc_start: 0.8298 (p0) cc_final: 0.7938 (p0) REVERT: J 104 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6184 (tmtt) REVERT: C 478 LYS cc_start: 0.7104 (mmtm) cc_final: 0.6108 (mtmm) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1639 time to fit residues: 16.6242 Evaluate side-chains 73 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.154164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121139 restraints weight = 6688.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.126355 restraints weight = 3549.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.129613 restraints weight = 2490.319| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3418 Z= 0.251 Angle : 0.703 12.028 4650 Z= 0.363 Chirality : 0.044 0.164 509 Planarity : 0.005 0.037 604 Dihedral : 5.227 23.656 496 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.31 % Rotamer: Outliers : 3.92 % Allowed : 22.41 % Favored : 73.67 % 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: -1.22 (0.42), residues: 426 helix: -3.17 (1.00), residues: 18 sheet: 0.62 (0.45), residues: 130 loop : -1.45 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 117 HIS 0.002 0.001 HIS J 96 PHE 0.015 0.001 PHE C 374 TYR 0.016 0.002 TYR J 31 ARG 0.004 0.001 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.68 seconds wall clock time: 30 minutes 10.67 seconds (1810.67 seconds total)