Starting phenix.real_space_refine on Fri Aug 22 13:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khd_37241/08_2025/8khd_37241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khd_37241/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8khd_37241/08_2025/8khd_37241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khd_37241/08_2025/8khd_37241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8khd_37241/08_2025/8khd_37241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khd_37241/08_2025/8khd_37241.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.29, per 1000 atoms: 0.39 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: 0.24 Conformation dependent library (CDL) restraints added in 108.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.11 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: 0.53 Time building geometry restraints manager: 0.35 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.610 Find NCS groups from input model: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3425 Z= 0.189 Angle : 0.884 11.654 4665 Z= 0.467 Chirality : 0.050 0.223 509 Planarity : 0.006 0.051 604 Dihedral : 13.417 88.113 1218 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG C 454 TYR 0.034 0.002 TYR C 369 PHE 0.039 0.002 PHE C 374 TRP 0.008 0.001 TRP C 353 HIS 0.002 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3418) covalent geometry : angle 0.87647 ( 4650) SS BOND : bond 0.01016 ( 6) SS BOND : angle 2.23600 ( 12) hydrogen bonds : bond 0.10069 ( 85) hydrogen bonds : angle 7.87130 ( 219) link_NAG-ASN : bond 0.00566 ( 1) link_NAG-ASN : angle 2.26007 ( 3) *********************** 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 : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0577 time to fit residues: 5.4817 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 : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.155296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122025 restraints weight = 6508.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.126925 restraints weight = 3565.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.130083 restraints weight = 2522.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.132007 restraints weight = 2040.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133467 restraints weight = 1778.513| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3425 Z= 0.160 Angle : 0.649 7.866 4665 Z= 0.339 Chirality : 0.043 0.178 509 Planarity : 0.005 0.039 604 Dihedral : 5.627 29.587 496 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.51 % Favored : 92.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.42), residues: 426 helix: -4.35 (0.67), residues: 19 sheet: 1.17 (0.48), residues: 123 loop : -1.64 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 509 TYR 0.012 0.002 TYR C 369 PHE 0.012 0.001 PHE C 377 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3418) covalent geometry : angle 0.63977 ( 4650) SS BOND : bond 0.00571 ( 6) SS BOND : angle 1.94874 ( 12) hydrogen bonds : bond 0.03474 ( 85) hydrogen bonds : angle 5.84759 ( 219) link_NAG-ASN : bond 0.00405 ( 1) link_NAG-ASN : angle 2.33052 ( 3) *********************** 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 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: H 107 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6399 (ptp) REVERT: J 48 TYR cc_start: 0.7429 (p90) cc_final: 0.7214 (p90) REVERT: J 69 THR cc_start: 0.8506 (p) cc_final: 0.8259 (p) REVERT: C 390 LEU cc_start: 0.7447 (pt) cc_final: 0.7029 (tt) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 0.0533 time to fit residues: 5.0274 Evaluate side-chains 64 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.151484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.122991 restraints weight = 6141.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.127527 restraints weight = 3388.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.130586 restraints weight = 2376.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.132606 restraints weight = 1887.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.134074 restraints weight = 1613.006| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3425 Z= 0.123 Angle : 0.608 8.223 4665 Z= 0.312 Chirality : 0.043 0.167 509 Planarity : 0.004 0.039 604 Dihedral : 5.223 27.114 496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.69 % Favored : 91.08 % Rotamer: Outliers : 1.96 % Allowed : 17.37 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.42), residues: 426 helix: -3.94 (0.83), residues: 18 sheet: 1.29 (0.49), residues: 119 loop : -1.58 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.013 0.001 TYR C 380 PHE 0.008 0.001 PHE C 338 TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3418) covalent geometry : angle 0.60198 ( 4650) SS BOND : bond 0.00867 ( 6) SS BOND : angle 1.42065 ( 12) hydrogen bonds : bond 0.03153 ( 85) hydrogen bonds : angle 5.60012 ( 219) link_NAG-ASN : bond 0.00453 ( 1) link_NAG-ASN : angle 2.06669 ( 3) *********************** 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 76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.7958 (m-30) cc_final: 0.7713 (m-30) REVERT: J 48 TYR cc_start: 0.7380 (p90) cc_final: 0.6751 (p90) REVERT: J 69 THR cc_start: 0.8532 (p) cc_final: 0.8195 (p) REVERT: C 390 LEU cc_start: 0.7196 (pt) cc_final: 0.6780 (tt) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.0400 time to fit residues: 3.6934 Evaluate side-chains 67 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 108 MET 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 24 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.143979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.114901 restraints weight = 6251.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119245 restraints weight = 3541.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.122166 restraints weight = 2517.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.124033 restraints weight = 2024.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.125192 restraints weight = 1754.228| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 3425 Z= 0.255 Angle : 0.741 8.132 4665 Z= 0.385 Chirality : 0.047 0.188 509 Planarity : 0.006 0.043 604 Dihedral : 6.158 31.702 496 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.86 % Favored : 89.91 % Rotamer: Outliers : 5.04 % Allowed : 17.09 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.42), residues: 426 helix: -3.79 (1.01), residues: 13 sheet: 1.14 (0.49), residues: 119 loop : -1.64 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 357 TYR 0.017 0.002 TYR C 369 PHE 0.013 0.002 PHE H 27 TRP 0.012 0.002 TRP C 436 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 3418) covalent geometry : angle 0.73148 ( 4650) SS BOND : bond 0.00806 ( 6) SS BOND : angle 1.94862 ( 12) hydrogen bonds : bond 0.04101 ( 85) hydrogen bonds : angle 5.93657 ( 219) link_NAG-ASN : bond 0.00522 ( 1) link_NAG-ASN : angle 2.88483 ( 3) *********************** 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 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.089 Fit side-chains REVERT: J 36 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: J 69 THR cc_start: 0.8504 (p) cc_final: 0.8209 (p) REVERT: C 360 ASN cc_start: 0.8804 (m-40) cc_final: 0.8600 (m110) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 0.0489 time to fit residues: 5.2617 Evaluate side-chains 77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 36 GLN 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 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 14 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117554 restraints weight = 6140.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122102 restraints weight = 3427.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.125118 restraints weight = 2422.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.126986 restraints weight = 1937.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.128325 restraints weight = 1679.420| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3425 Z= 0.147 Angle : 0.674 8.357 4665 Z= 0.348 Chirality : 0.045 0.182 509 Planarity : 0.005 0.039 604 Dihedral : 5.755 30.323 496 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 4.20 % Allowed : 17.93 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.42), residues: 426 helix: -4.12 (0.67), residues: 19 sheet: 1.16 (0.48), residues: 119 loop : -1.65 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 355 TYR 0.016 0.002 TYR J 48 PHE 0.010 0.001 PHE C 400 TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3418) covalent geometry : angle 0.66307 ( 4650) SS BOND : bond 0.00816 ( 6) SS BOND : angle 2.14859 ( 12) hydrogen bonds : bond 0.03323 ( 85) hydrogen bonds : angle 5.69430 ( 219) link_NAG-ASN : bond 0.00492 ( 1) link_NAG-ASN : angle 2.64128 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.144 Fit side-chains REVERT: J 69 THR cc_start: 0.8510 (p) cc_final: 0.8209 (p) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.0541 time to fit residues: 5.3288 Evaluate side-chains 71 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE 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 37 optimal weight: 0.0670 chunk 1 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.0050 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.3548 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.149114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.120467 restraints weight = 6139.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.125099 restraints weight = 3416.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.127983 restraints weight = 2415.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.130033 restraints weight = 1943.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.131377 restraints weight = 1667.950| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3425 Z= 0.111 Angle : 0.630 8.378 4665 Z= 0.323 Chirality : 0.044 0.159 509 Planarity : 0.004 0.037 604 Dihedral : 5.319 27.716 496 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 1.68 % Allowed : 21.01 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.42), residues: 426 helix: -3.86 (0.76), residues: 19 sheet: 1.18 (0.49), residues: 119 loop : -1.49 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.020 0.001 TYR J 48 PHE 0.010 0.001 PHE C 338 TRP 0.005 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3418) covalent geometry : angle 0.61957 ( 4650) SS BOND : bond 0.00546 ( 6) SS BOND : angle 2.03431 ( 12) hydrogen bonds : bond 0.02839 ( 85) hydrogen bonds : angle 5.34008 ( 219) link_NAG-ASN : bond 0.00471 ( 1) link_NAG-ASN : angle 2.45448 ( 3) *********************** 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 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.094 Fit side-chains REVERT: J 69 THR cc_start: 0.8511 (p) cc_final: 0.8231 (p) REVERT: C 390 LEU cc_start: 0.7250 (pt) cc_final: 0.6881 (tt) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.0736 time to fit residues: 6.8009 Evaluate side-chains 68 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 GLN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110172 restraints weight = 6583.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.114419 restraints weight = 3749.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.117110 restraints weight = 2736.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.118729 restraints weight = 2259.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119977 restraints weight = 2002.570| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.119 3425 Z= 0.436 Angle : 0.933 8.869 4665 Z= 0.497 Chirality : 0.053 0.214 509 Planarity : 0.007 0.051 604 Dihedral : 7.168 40.050 496 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.74 % Favored : 88.03 % Rotamer: Outliers : 8.68 % Allowed : 18.49 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.41), residues: 426 helix: -4.07 (0.59), residues: 27 sheet: 0.60 (0.48), residues: 119 loop : -2.04 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 355 TYR 0.019 0.003 TYR J 86 PHE 0.020 0.003 PHE C 400 TRP 0.011 0.002 TRP C 436 HIS 0.005 0.002 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.01016 ( 3418) covalent geometry : angle 0.91557 ( 4650) SS BOND : bond 0.01217 ( 6) SS BOND : angle 3.25738 ( 12) hydrogen bonds : bond 0.05281 ( 85) hydrogen bonds : angle 6.65821 ( 219) link_NAG-ASN : bond 0.00751 ( 1) link_NAG-ASN : angle 3.43030 ( 3) *********************** 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 104 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: J 69 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8236 (p) REVERT: J 104 LYS cc_start: 0.7383 (ttmm) cc_final: 0.6367 (tmtt) REVERT: C 357 ARG cc_start: 0.8179 (tmm-80) cc_final: 0.7772 (ttm-80) outliers start: 31 outliers final: 28 residues processed: 92 average time/residue: 0.0458 time to fit residues: 5.1875 Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 109 TYR 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 69 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 377 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 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 466 ARG 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 524 VAL 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 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 439 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 = 0.4194 r_free = 0.4194 target = 0.147796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118455 restraints weight = 6584.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.123262 restraints weight = 3572.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.126384 restraints weight = 2522.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128329 restraints weight = 2027.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.129667 restraints weight = 1764.049| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3425 Z= 0.134 Angle : 0.716 8.716 4665 Z= 0.372 Chirality : 0.045 0.166 509 Planarity : 0.004 0.038 604 Dihedral : 5.859 33.195 496 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 3.36 % Allowed : 23.81 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.42), residues: 426 helix: -3.58 (0.85), residues: 18 sheet: 0.41 (0.47), residues: 128 loop : -1.63 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.019 0.001 TYR J 48 PHE 0.008 0.001 PHE C 338 TRP 0.007 0.001 TRP H 36 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3418) covalent geometry : angle 0.70436 ( 4650) SS BOND : bond 0.00675 ( 6) SS BOND : angle 2.07754 ( 12) hydrogen bonds : bond 0.03274 ( 85) hydrogen bonds : angle 5.68933 ( 219) link_NAG-ASN : bond 0.00540 ( 1) link_NAG-ASN : angle 3.24732 ( 3) *********************** 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: 12 poor density : 76 time to evaluate : 0.077 Fit side-chains REVERT: H 109 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6781 (t80) REVERT: J 48 TYR cc_start: 0.7736 (p90) cc_final: 0.7415 (p90) REVERT: J 69 THR cc_start: 0.8478 (p) cc_final: 0.8177 (p) REVERT: C 357 ARG cc_start: 0.8069 (tmm-80) cc_final: 0.7605 (ttm-80) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.0558 time to fit residues: 5.7176 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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 36 GLN Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 439 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 = 0.4130 r_free = 0.4130 target = 0.143129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.113354 restraints weight = 6352.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117956 restraints weight = 3562.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120933 restraints weight = 2551.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.122830 restraints weight = 2073.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.123928 restraints weight = 1807.966| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3425 Z= 0.197 Angle : 0.743 9.464 4665 Z= 0.384 Chirality : 0.046 0.188 509 Planarity : 0.005 0.037 604 Dihedral : 6.064 35.440 496 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.03 % Favored : 88.73 % Rotamer: Outliers : 4.48 % Allowed : 21.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.41), residues: 426 helix: -4.20 (0.55), residues: 25 sheet: 0.67 (0.48), residues: 119 loop : -1.75 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.016 0.002 TYR J 31 PHE 0.019 0.002 PHE C 374 TRP 0.010 0.001 TRP J 34 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3418) covalent geometry : angle 0.72788 ( 4650) SS BOND : bond 0.00892 ( 6) SS BOND : angle 2.63270 ( 12) hydrogen bonds : bond 0.03704 ( 85) hydrogen bonds : angle 5.76543 ( 219) link_NAG-ASN : bond 0.00584 ( 1) link_NAG-ASN : angle 3.17705 ( 3) *********************** 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 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.140 Fit side-chains REVERT: H 109 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7004 (t80) REVERT: J 69 THR cc_start: 0.8562 (p) cc_final: 0.8271 (p) REVERT: C 357 ARG cc_start: 0.8120 (tmm-80) cc_final: 0.7621 (ttm-80) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.0568 time to fit residues: 5.3821 Evaluate side-chains 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 109 TYR Chi-restraints excluded: chain H residue 123 VAL 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 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 23 GLN J 36 GLN ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.146289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.116773 restraints weight = 6375.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121542 restraints weight = 3492.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124651 restraints weight = 2479.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.126642 restraints weight = 2005.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.127919 restraints weight = 1746.914| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3425 Z= 0.150 Angle : 0.722 8.877 4665 Z= 0.371 Chirality : 0.045 0.171 509 Planarity : 0.004 0.037 604 Dihedral : 5.828 33.420 496 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 4.20 % Allowed : 23.25 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.42), residues: 426 helix: -3.96 (0.72), residues: 19 sheet: 0.40 (0.46), residues: 128 loop : -1.63 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.018 0.001 TYR J 48 PHE 0.015 0.001 PHE C 374 TRP 0.005 0.001 TRP H 36 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3418) covalent geometry : angle 0.70958 ( 4650) SS BOND : bond 0.00869 ( 6) SS BOND : angle 2.31432 ( 12) hydrogen bonds : bond 0.03271 ( 85) hydrogen bonds : angle 5.64577 ( 219) link_NAG-ASN : bond 0.00605 ( 1) link_NAG-ASN : angle 3.04285 ( 3) ********************** 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 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.123 Fit side-chains REVERT: H 109 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6798 (t80) REVERT: J 69 THR cc_start: 0.8520 (p) cc_final: 0.8227 (p) REVERT: J 104 LYS cc_start: 0.7148 (ttmm) cc_final: 0.6251 (tmtt) REVERT: C 357 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7672 (ttm-80) outliers start: 15 outliers final: 14 residues processed: 76 average time/residue: 0.0535 time to fit residues: 4.9735 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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 109 TYR 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 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR 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 1 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 30 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 23 GLN ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.145200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.115708 restraints weight = 6505.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.120111 restraints weight = 3774.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123041 restraints weight = 2735.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.124953 restraints weight = 2231.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.126252 restraints weight = 1947.702| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3425 Z= 0.139 Angle : 0.709 8.995 4665 Z= 0.362 Chirality : 0.045 0.160 509 Planarity : 0.004 0.036 604 Dihedral : 5.625 32.834 496 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.39 % Favored : 90.38 % Rotamer: Outliers : 3.92 % Allowed : 24.09 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.42), residues: 426 helix: -3.91 (0.77), residues: 19 sheet: 0.44 (0.46), residues: 130 loop : -1.55 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.018 0.001 TYR J 48 PHE 0.014 0.001 PHE C 374 TRP 0.010 0.001 TRP J 34 HIS 0.002 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3418) covalent geometry : angle 0.69813 ( 4650) SS BOND : bond 0.00785 ( 6) SS BOND : angle 2.16851 ( 12) hydrogen bonds : bond 0.03175 ( 85) hydrogen bonds : angle 5.48449 ( 219) link_NAG-ASN : bond 0.00575 ( 1) link_NAG-ASN : angle 2.88845 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 755.75 seconds wall clock time: 13 minutes 39.91 seconds (819.91 seconds total)