Starting phenix.real_space_refine on Wed Mar 5 19:12:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khd_37241/03_2025/8khd_37241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khd_37241/03_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_37241/03_2025/8khd_37241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khd_37241/03_2025/8khd_37241.map" model { file = "/net/cci-nas-00/data/ceres_data/8khd_37241/03_2025/8khd_37241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khd_37241/03_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-5624/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: 4.09, per 1000 atoms: 1.23 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: 0.91 Conformation dependent library (CDL) restraints added in 412.2 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: 0.35 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: 0.76 Time building geometry restraints manager: 0.95 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: 2.850 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- 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 : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1711 time to fit residues: 16.1099 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 : 0.341 ------------------------------------------------------------------------------- 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 = 0.120895 restraints weight = 6478.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.125524 restraints weight = 3557.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.128859 restraints weight = 2538.889| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.391 Fit side-chains REVERT: H 107 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6529 (ptp) REVERT: J 48 TYR cc_start: 0.7490 (p90) cc_final: 0.7233 (p90) REVERT: C 360 ASN cc_start: 0.8683 (m-40) cc_final: 0.8397 (m-40) REVERT: C 390 LEU cc_start: 0.7520 (pt) cc_final: 0.7085 (tt) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.1359 time to fit residues: 12.1403 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 : 0.377 ------------------------------------------------------------------------------- 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: 0.0970 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 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: 4.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.155654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.123403 restraints weight = 6275.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128069 restraints weight = 3473.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131235 restraints weight = 2452.591| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3418 Z= 0.182 Angle : 0.601 8.069 4650 Z= 0.309 Chirality : 0.043 0.168 509 Planarity : 0.004 0.040 604 Dihedral : 5.255 27.325 496 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 1.96 % Allowed : 18.21 % 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: -1.05 (0.41), residues: 426 helix: -3.52 (1.23), residues: 12 sheet: 1.28 (0.48), residues: 119 loop : -1.55 (0.36), residues: 295 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 0.014 0.001 TYR C 380 ARG 0.002 0.000 ARG C 403 *********************** 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 74 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.7948 (m-30) cc_final: 0.7717 (m-30) REVERT: J 68 ASN cc_start: 0.8345 (p0) cc_final: 0.8127 (p0) REVERT: C 360 ASN cc_start: 0.8674 (m-40) cc_final: 0.8434 (m-40) REVERT: C 390 LEU cc_start: 0.7369 (pt) cc_final: 0.6902 (tt) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.1344 time to fit residues: 11.9272 Evaluate side-chains 65 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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: 0.0370 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.4074 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.147399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118140 restraints weight = 6243.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.122621 restraints weight = 3503.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.125622 restraints weight = 2480.637| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3418 Z= 0.258 Angle : 0.639 7.884 4650 Z= 0.331 Chirality : 0.044 0.173 509 Planarity : 0.005 0.039 604 Dihedral : 5.459 27.816 496 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.86 % Favored : 89.91 % Rotamer: Outliers : 3.64 % Allowed : 17.93 % 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: -1.07 (0.42), residues: 426 helix: -3.65 (1.15), residues: 13 sheet: 1.20 (0.48), residues: 120 loop : -1.52 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.013 0.001 PHE C 338 TYR 0.017 0.002 TYR C 369 ARG 0.005 0.001 ARG C 357 *********************** 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 84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.343 Fit side-chains REVERT: J 48 TYR cc_start: 0.7555 (p90) cc_final: 0.7085 (p90) REVERT: J 68 ASN cc_start: 0.8340 (p0) cc_final: 0.7991 (p0) REVERT: C 360 ASN cc_start: 0.8776 (m-40) cc_final: 0.8571 (m110) outliers start: 13 outliers final: 8 residues processed: 78 average time/residue: 0.1247 time to fit residues: 12.4062 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain J residue 7 ASP 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 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: 2.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.146559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117497 restraints weight = 6216.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122010 restraints weight = 3470.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.124997 restraints weight = 2455.747| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3418 Z= 0.276 Angle : 0.666 8.260 4650 Z= 0.345 Chirality : 0.045 0.183 509 Planarity : 0.005 0.037 604 Dihedral : 5.696 28.815 496 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.86 % Favored : 89.91 % Rotamer: Outliers : 5.60 % Allowed : 15.97 % 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: -1.08 (0.42), residues: 426 helix: -3.59 (1.06), residues: 13 sheet: 1.25 (0.49), residues: 119 loop : -1.55 (0.37), residues: 294 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 0.009 0.001 PHE C 400 TYR 0.011 0.001 TYR J 31 ARG 0.003 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 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.352 Fit side-chains REVERT: H 119 GLN cc_start: 0.7372 (pp30) cc_final: 0.7046 (pp30) REVERT: J 68 ASN cc_start: 0.8349 (p0) cc_final: 0.7972 (p0) REVERT: J 104 LYS cc_start: 0.7072 (ttmm) cc_final: 0.6119 (tmtt) REVERT: C 360 ASN cc_start: 0.8754 (m-40) cc_final: 0.8544 (m110) REVERT: C 390 LEU cc_start: 0.7335 (pt) cc_final: 0.6742 (tt) REVERT: C 406 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6779 (mp0) outliers start: 20 outliers final: 15 residues processed: 87 average time/residue: 0.1340 time to fit residues: 14.6383 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 36 GLN 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 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: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.146563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117561 restraints weight = 6361.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122057 restraints weight = 3514.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.125069 restraints weight = 2481.167| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3055 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= 0.245 Angle : 0.640 7.898 4650 Z= 0.331 Chirality : 0.045 0.165 509 Planarity : 0.004 0.036 604 Dihedral : 5.554 29.168 496 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.86 % Favored : 89.91 % Rotamer: Outliers : 4.76 % Allowed : 18.77 % 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: -1.23 (0.42), residues: 426 helix: -3.95 (0.75), residues: 19 sheet: 1.15 (0.49), residues: 119 loop : -1.58 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 J 48 ARG 0.002 0.000 ARG C 509 *********************** 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 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.379 Fit side-chains REVERT: H 119 GLN cc_start: 0.7409 (pp30) cc_final: 0.7122 (pp30) REVERT: J 68 ASN cc_start: 0.8342 (p0) cc_final: 0.8095 (p0) REVERT: J 104 LYS cc_start: 0.7093 (ttmm) cc_final: 0.6173 (tmtt) REVERT: C 360 ASN cc_start: 0.8716 (m-40) cc_final: 0.8515 (m110) REVERT: C 390 LEU cc_start: 0.7472 (pt) cc_final: 0.6987 (tt) REVERT: C 406 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6768 (mp0) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.1367 time to fit residues: 14.0008 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 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 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: 1.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.146720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117946 restraints weight = 6206.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.122447 restraints weight = 3471.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.125489 restraints weight = 2455.020| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3166 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= 0.229 Angle : 0.646 8.540 4650 Z= 0.333 Chirality : 0.045 0.163 509 Planarity : 0.005 0.036 604 Dihedral : 5.477 29.311 496 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.61 % Rotamer: Outliers : 5.60 % Allowed : 19.05 % 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: -1.23 (0.42), residues: 426 helix: -3.61 (0.84), residues: 19 sheet: 1.06 (0.48), residues: 119 loop : -1.56 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS J 96 PHE 0.008 0.001 PHE C 400 TYR 0.017 0.002 TYR J 48 ARG 0.003 0.000 ARG J 19 *********************** 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 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.362 Fit side-chains REVERT: H 92 ASP cc_start: 0.8138 (m-30) cc_final: 0.7905 (m-30) REVERT: H 119 GLN cc_start: 0.7434 (pp30) cc_final: 0.7150 (pp30) REVERT: J 68 ASN cc_start: 0.8333 (p0) cc_final: 0.8069 (p0) REVERT: J 104 LYS cc_start: 0.7089 (ttmm) cc_final: 0.6187 (tmtt) REVERT: C 406 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6813 (mp0) outliers start: 20 outliers final: 16 residues processed: 84 average time/residue: 0.1425 time to fit residues: 15.1412 Evaluate side-chains 84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE 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 406 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 433 VAL 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: 0.7980 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 0.0170 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.154237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.122236 restraints weight = 6528.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.127043 restraints weight = 3540.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.130271 restraints weight = 2486.278| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3418 Z= 0.173 Angle : 0.630 8.618 4650 Z= 0.322 Chirality : 0.044 0.158 509 Planarity : 0.004 0.036 604 Dihedral : 5.120 27.443 496 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 3.08 % Allowed : 22.13 % 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: -1.10 (0.43), residues: 426 helix: -3.39 (0.95), residues: 19 sheet: 0.96 (0.47), residues: 123 loop : -1.41 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 34 HIS 0.002 0.001 HIS J 96 PHE 0.007 0.001 PHE C 338 TYR 0.013 0.001 TYR C 380 ARG 0.003 0.000 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 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 119 GLN cc_start: 0.7372 (pp30) cc_final: 0.7138 (pp30) REVERT: J 51 ASN cc_start: 0.7462 (p0) cc_final: 0.7253 (t0) REVERT: J 68 ASN cc_start: 0.8322 (p0) cc_final: 0.7896 (p0) REVERT: J 104 LYS cc_start: 0.7022 (ttmm) cc_final: 0.6138 (tmtt) REVERT: C 406 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6744 (mp0) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.1509 time to fit residues: 15.2679 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 433 VAL 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: 0.8980 chunk 35 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.149664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.120908 restraints weight = 6327.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.125558 restraints weight = 3486.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.128638 restraints weight = 2458.167| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3418 Z= 0.184 Angle : 0.646 8.912 4650 Z= 0.328 Chirality : 0.044 0.157 509 Planarity : 0.004 0.036 604 Dihedral : 5.092 26.867 496 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 3.36 % Allowed : 22.97 % 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: -1.01 (0.42), residues: 426 helix: -3.44 (0.91), residues: 19 sheet: 1.10 (0.48), residues: 121 loop : -1.37 (0.39), residues: 286 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 0.012 0.001 PHE C 374 TYR 0.019 0.001 TYR J 48 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 84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.8124 (m-30) cc_final: 0.7920 (m-30) REVERT: J 48 TYR cc_start: 0.7487 (p90) cc_final: 0.7047 (p90) REVERT: J 68 ASN cc_start: 0.8286 (p0) cc_final: 0.7892 (p0) REVERT: J 104 LYS cc_start: 0.7067 (ttmm) cc_final: 0.6199 (tmtt) REVERT: C 357 ARG cc_start: 0.8093 (tmm-80) cc_final: 0.7673 (ttt180) REVERT: C 406 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6633 (mp0) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1507 time to fit residues: 14.4064 Evaluate side-chains 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.150283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.121439 restraints weight = 6345.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.126157 restraints weight = 3458.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.129252 restraints weight = 2430.026| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3418 Z= 0.193 Angle : 0.673 8.652 4650 Z= 0.343 Chirality : 0.044 0.158 509 Planarity : 0.004 0.036 604 Dihedral : 5.007 25.490 496 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 2.80 % Allowed : 24.09 % Favored : 73.11 % 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: -0.86 (0.42), residues: 426 helix: -2.83 (1.25), residues: 13 sheet: 1.12 (0.48), residues: 121 loop : -1.31 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 34 HIS 0.002 0.001 HIS J 96 PHE 0.012 0.001 PHE C 374 TYR 0.019 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 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: J 48 TYR cc_start: 0.7535 (p90) cc_final: 0.7130 (p90) REVERT: J 68 ASN cc_start: 0.8299 (p0) cc_final: 0.7897 (p0) REVERT: J 104 LYS cc_start: 0.7049 (ttmm) cc_final: 0.6196 (tmtt) REVERT: C 357 ARG cc_start: 0.8031 (tmm-80) cc_final: 0.7707 (ttt180) REVERT: C 406 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6710 (mp0) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1535 time to fit residues: 13.7135 Evaluate side-chains 75 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL 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: 3.9990 chunk 27 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 23 GLN J 68 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 = 0.154246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.122064 restraints weight = 6641.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.126901 restraints weight = 3581.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.130127 restraints weight = 2531.352| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3418 Z= 0.226 Angle : 0.686 9.184 4650 Z= 0.348 Chirality : 0.044 0.161 509 Planarity : 0.004 0.039 604 Dihedral : 5.231 25.897 496 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.69 % Favored : 91.08 % Rotamer: Outliers : 3.64 % Allowed : 22.13 % Favored : 74.23 % 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: -3.37 (0.90), residues: 18 sheet: 0.98 (0.47), residues: 121 loop : -1.30 (0.39), residues: 287 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 0.012 0.001 PHE C 374 TYR 0.017 0.001 TYR J 48 ARG 0.002 0.000 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.69 seconds wall clock time: 29 minutes 48.24 seconds (1788.24 seconds total)