Starting phenix.real_space_refine on Wed Sep 17 03:22:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asd_43813/09_2025/9asd_43813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asd_43813/09_2025/9asd_43813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asd_43813/09_2025/9asd_43813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asd_43813/09_2025/9asd_43813.map" model { file = "/net/cci-nas-00/data/ceres_data/9asd_43813/09_2025/9asd_43813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asd_43813/09_2025/9asd_43813.cif" } resolution = 3.3 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= -0.000 sd= 0.038 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 15 5.16 5 C 1964 2.51 5 N 513 2.21 5 O 521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3013 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 837 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 738 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1410 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain breaks: 2 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.98, per 1000 atoms: 0.33 Number of scatterers: 3013 At special positions: 0 Unit cell: (64, 68, 90, 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 15 16.00 O 521 8.00 N 513 7.00 C 1964 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 96 " distance=2.09 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.17 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.17 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.28 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R1301 " - " ASN R 343 " " NAG R1302 " - " ASN R 354 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 107.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 7.2% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.922A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.876A pdb=" N SER R 408 " --> pdb=" O ASN R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.474A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.474A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.344A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.022A pdb=" N ILE L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.173A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 114 hydrogen bonds defined for protein. 273 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: 0.47 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 476 1.26 - 1.41: 935 1.41 - 1.57: 1670 1.57 - 1.72: 5 1.72 - 1.87: 18 Bond restraints: 3104 Sorted by residual: bond pdb=" C LYS R 403 " pdb=" O LYS R 403 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.25e-02 6.40e+03 9.68e+01 bond pdb=" CA LYS R 403 " pdb=" C LYS R 403 " ideal model delta sigma weight residual 1.524 1.444 0.080 1.31e-02 5.83e+03 3.77e+01 bond pdb=" C LYS R 403 " pdb=" N GLY R 404 " ideal model delta sigma weight residual 1.334 1.262 0.072 1.32e-02 5.74e+03 2.99e+01 bond pdb=" C MET L 49 " pdb=" O MET L 49 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" C ILE L 50 " pdb=" O ILE L 50 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.11e-02 8.12e+03 1.42e+01 ... (remaining 3099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 3961 2.53 - 5.06: 209 5.06 - 7.59: 60 7.59 - 10.12: 12 10.12 - 12.65: 4 Bond angle restraints: 4246 Sorted by residual: angle pdb=" N ALA L 82 " pdb=" CA ALA L 82 " pdb=" C ALA L 82 " ideal model delta sigma weight residual 112.38 121.88 -9.50 1.22e+00 6.72e-01 6.06e+01 angle pdb=" N SER R 469 " pdb=" CA SER R 469 " pdb=" C SER R 469 " ideal model delta sigma weight residual 109.40 96.75 12.65 1.63e+00 3.76e-01 6.02e+01 angle pdb=" C GLY R 526 " pdb=" N PRO R 527 " pdb=" CA PRO R 527 " ideal model delta sigma weight residual 119.76 127.64 -7.88 1.03e+00 9.43e-01 5.86e+01 angle pdb=" C TYR H 101 " pdb=" N PRO H 102 " pdb=" CA PRO H 102 " ideal model delta sigma weight residual 120.21 127.29 -7.08 9.60e-01 1.09e+00 5.44e+01 angle pdb=" N ASP L 84 " pdb=" CA ASP L 84 " pdb=" C ASP L 84 " ideal model delta sigma weight residual 113.17 104.03 9.14 1.26e+00 6.30e-01 5.26e+01 ... (remaining 4241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 1666 15.04 - 30.08: 90 30.08 - 45.12: 29 45.12 - 60.15: 5 60.15 - 75.19: 3 Dihedral angle restraints: 1793 sinusoidal: 582 harmonic: 1211 Sorted by residual: dihedral pdb=" C LYS R 403 " pdb=" N LYS R 403 " pdb=" CA LYS R 403 " pdb=" CB LYS R 403 " ideal model delta harmonic sigma weight residual -122.60 -102.68 -19.92 0 2.50e+00 1.60e-01 6.35e+01 dihedral pdb=" N VAL L 53 " pdb=" C VAL L 53 " pdb=" CA VAL L 53 " pdb=" CB VAL L 53 " ideal model delta harmonic sigma weight residual 123.40 140.49 -17.09 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" C ILE R 468 " pdb=" N ILE R 468 " pdb=" CA ILE R 468 " pdb=" CB ILE R 468 " ideal model delta harmonic sigma weight residual -122.00 -106.29 -15.71 0 2.50e+00 1.60e-01 3.95e+01 ... (remaining 1790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 389 0.114 - 0.227: 46 0.227 - 0.340: 8 0.340 - 0.453: 0 0.453 - 0.567: 3 Chirality restraints: 446 Sorted by residual: chirality pdb=" CA VAL L 53 " pdb=" N VAL L 53 " pdb=" C VAL L 53 " pdb=" CB VAL L 53 " both_signs ideal model delta sigma weight residual False 2.44 1.87 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CB VAL L 53 " pdb=" CA VAL L 53 " pdb=" CG1 VAL L 53 " pdb=" CG2 VAL L 53 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ILE R 468 " pdb=" N ILE R 468 " pdb=" C ILE R 468 " pdb=" CB ILE R 468 " both_signs ideal model delta sigma weight residual False 2.43 2.99 -0.55 2.00e-01 2.50e+01 7.61e+00 ... (remaining 443 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 56 " -0.736 9.50e-02 1.11e+02 3.30e-01 6.64e+01 pdb=" NE ARG L 56 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG L 56 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG L 56 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 56 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 87 " -0.534 9.50e-02 1.11e+02 2.39e-01 3.52e+01 pdb=" NE ARG H 87 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG H 87 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG H 87 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 87 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 402 " 0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C ILE R 402 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE R 402 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS R 403 " 0.024 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1063 2.86 - 3.37: 2296 3.37 - 3.88: 4814 3.88 - 4.39: 5605 4.39 - 4.90: 9585 Nonbonded interactions: 23363 Sorted by model distance: nonbonded pdb=" N LYS R 403 " pdb=" O LYS R 403 " model vdw 2.348 2.496 nonbonded pdb=" O ASN R 417 " pdb=" OD1 ASN R 417 " model vdw 2.382 3.040 nonbonded pdb=" O CYS R 480 " pdb=" C LYS R 481 " model vdw 2.454 3.270 nonbonded pdb=" N GLN R 493 " pdb=" O GLN R 493 " model vdw 2.461 2.496 nonbonded pdb=" OH TYR H 108 " pdb=" O LEU R 455 " model vdw 2.468 3.040 ... (remaining 23358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.460 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.310 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.012 0.252 3112 Z= 0.715 Angle : 1.534 14.758 4264 Z= 1.030 Chirality : 0.090 0.567 446 Planarity : 0.018 0.330 556 Dihedral : 11.034 75.192 1013 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.35 % Allowed : 4.04 % Favored : 94.62 % Cbeta Deviations : 1.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.14 (0.39), residues: 409 helix: -4.09 (0.64), residues: 14 sheet: 0.63 (0.39), residues: 143 loop : 0.11 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 87 TYR 0.038 0.005 TYR L 51 PHE 0.015 0.003 PHE L 48 TRP 0.020 0.004 TRP H 47 HIS 0.001 0.000 HIS L 41 Details of bonding type rmsd covalent geometry : bond 0.01070 ( 3104) covalent geometry : angle 1.50585 ( 4246) SS BOND : bond 0.13363 ( 6) SS BOND : angle 5.54497 ( 12) hydrogen bonds : bond 0.16298 ( 100) hydrogen bonds : angle 9.10659 ( 273) link_NAG-ASN : bond 0.06304 ( 2) link_NAG-ASN : angle 2.31803 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.114 Fit side-chains REVERT: L 52 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7792 (t70) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.0872 time to fit residues: 5.6762 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158371 restraints weight = 4066.742| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.70 r_work: 0.3803 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3112 Z= 0.116 Angle : 0.587 6.062 4264 Z= 0.310 Chirality : 0.048 0.231 446 Planarity : 0.004 0.034 556 Dihedral : 4.783 50.865 508 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.14 % Allowed : 5.38 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.45 (0.41), residues: 409 helix: -3.49 (1.11), residues: 14 sheet: 0.95 (0.40), residues: 146 loop : 0.21 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 346 TYR 0.023 0.002 TYR H 35 PHE 0.014 0.002 PHE R 377 TRP 0.015 0.001 TRP H 47 HIS 0.001 0.000 HIS L 41 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3104) covalent geometry : angle 0.58229 ( 4246) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.29747 ( 12) hydrogen bonds : bond 0.03229 ( 100) hydrogen bonds : angle 6.38666 ( 273) link_NAG-ASN : bond 0.00266 ( 2) link_NAG-ASN : angle 1.40073 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: H 110 LEU cc_start: 0.8897 (mt) cc_final: 0.8641 (mt) REVERT: L 52 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7929 (t70) outliers start: 7 outliers final: 1 residues processed: 48 average time/residue: 0.0851 time to fit residues: 4.7921 Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 8 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.0030 chunk 4 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 0.1306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157066 restraints weight = 4020.674| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.53 r_work: 0.3816 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3112 Z= 0.093 Angle : 0.535 6.668 4264 Z= 0.279 Chirality : 0.047 0.260 446 Planarity : 0.004 0.032 556 Dihedral : 4.546 51.931 508 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.35 % Allowed : 10.31 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.50 (0.41), residues: 409 helix: -3.69 (0.82), residues: 14 sheet: 1.13 (0.41), residues: 145 loop : 0.16 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 346 TYR 0.022 0.001 TYR H 35 PHE 0.012 0.001 PHE R 400 TRP 0.010 0.001 TRP H 47 HIS 0.000 0.000 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 3104) covalent geometry : angle 0.52954 ( 4246) SS BOND : bond 0.00332 ( 6) SS BOND : angle 1.30155 ( 12) hydrogen bonds : bond 0.02884 ( 100) hydrogen bonds : angle 5.86393 ( 273) link_NAG-ASN : bond 0.00306 ( 2) link_NAG-ASN : angle 1.25306 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7866 (t70) REVERT: R 501 TYR cc_start: 0.6748 (m-10) cc_final: 0.6543 (m-10) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.0840 time to fit residues: 4.3133 Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148679 restraints weight = 4084.445| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.73 r_work: 0.3685 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3112 Z= 0.183 Angle : 0.625 7.121 4264 Z= 0.320 Chirality : 0.048 0.251 446 Planarity : 0.004 0.042 556 Dihedral : 4.889 52.567 508 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.39 (0.41), residues: 409 helix: -3.69 (0.78), residues: 14 sheet: 1.17 (0.41), residues: 151 loop : -0.04 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.022 0.002 TYR R 495 PHE 0.012 0.002 PHE R 377 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 3104) covalent geometry : angle 0.61446 ( 4246) SS BOND : bond 0.00441 ( 6) SS BOND : angle 1.93094 ( 12) hydrogen bonds : bond 0.03071 ( 100) hydrogen bonds : angle 5.88724 ( 273) link_NAG-ASN : bond 0.00176 ( 2) link_NAG-ASN : angle 1.79467 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (t70) REVERT: L 84 ASP cc_start: 0.8334 (m-30) cc_final: 0.8101 (m-30) REVERT: R 462 LYS cc_start: 0.8267 (mttt) cc_final: 0.8003 (ttmm) outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 0.0837 time to fit residues: 4.4028 Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.0010 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153323 restraints weight = 4052.685| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.75 r_work: 0.3719 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3112 Z= 0.091 Angle : 0.533 6.544 4264 Z= 0.273 Chirality : 0.046 0.215 446 Planarity : 0.004 0.036 556 Dihedral : 4.601 53.930 508 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.24 % Allowed : 12.56 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.56 (0.42), residues: 409 helix: -3.72 (0.78), residues: 14 sheet: 1.36 (0.43), residues: 145 loop : 0.07 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 346 TYR 0.020 0.001 TYR H 35 PHE 0.012 0.001 PHE R 400 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 3104) covalent geometry : angle 0.52642 ( 4246) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.42937 ( 12) hydrogen bonds : bond 0.02628 ( 100) hydrogen bonds : angle 5.44473 ( 273) link_NAG-ASN : bond 0.00188 ( 2) link_NAG-ASN : angle 1.34028 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7983 (t70) REVERT: L 84 ASP cc_start: 0.8274 (m-30) cc_final: 0.8030 (m-30) REVERT: R 462 LYS cc_start: 0.8237 (mttt) cc_final: 0.8005 (ttmm) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.0796 time to fit residues: 4.5142 Evaluate side-chains 44 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138409 restraints weight = 4219.976| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.98 r_work: 0.3539 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3112 Z= 0.235 Angle : 0.662 7.405 4264 Z= 0.337 Chirality : 0.049 0.241 446 Planarity : 0.005 0.047 556 Dihedral : 5.158 52.857 508 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.69 % Allowed : 11.66 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.41), residues: 409 helix: -3.61 (0.84), residues: 14 sheet: 1.31 (0.42), residues: 149 loop : -0.16 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 346 TYR 0.029 0.002 TYR H 35 PHE 0.012 0.002 PHE L 48 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 41 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 3104) covalent geometry : angle 0.65144 ( 4246) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.92741 ( 12) hydrogen bonds : bond 0.03229 ( 100) hydrogen bonds : angle 5.90322 ( 273) link_NAG-ASN : bond 0.00161 ( 2) link_NAG-ASN : angle 2.01822 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.118 Fit side-chains REVERT: L 52 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8090 (t70) REVERT: L 84 ASP cc_start: 0.8412 (m-30) cc_final: 0.8187 (m-30) REVERT: R 462 LYS cc_start: 0.8224 (mttt) cc_final: 0.7961 (ttmm) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.0868 time to fit residues: 3.8249 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.0370 chunk 20 optimal weight: 0.0470 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 1 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141767 restraints weight = 4201.831| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.94 r_work: 0.3596 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3112 Z= 0.106 Angle : 0.555 6.438 4264 Z= 0.284 Chirality : 0.046 0.221 446 Planarity : 0.004 0.042 556 Dihedral : 4.722 53.188 508 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.69 % Favored : 97.07 % Rotamer: Outliers : 2.69 % Allowed : 13.45 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.48 (0.42), residues: 409 helix: -3.69 (0.75), residues: 14 sheet: 1.32 (0.42), residues: 149 loop : -0.03 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 346 TYR 0.018 0.001 TYR H 59 PHE 0.012 0.001 PHE R 400 TRP 0.011 0.001 TRP H 47 HIS 0.000 0.000 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3104) covalent geometry : angle 0.54656 ( 4246) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.57662 ( 12) hydrogen bonds : bond 0.02671 ( 100) hydrogen bonds : angle 5.43820 ( 273) link_NAG-ASN : bond 0.00149 ( 2) link_NAG-ASN : angle 1.53505 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.120 Fit side-chains REVERT: L 52 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8009 (t70) REVERT: L 84 ASP cc_start: 0.8287 (m-30) cc_final: 0.8035 (m-30) REVERT: R 462 LYS cc_start: 0.8215 (mttt) cc_final: 0.7953 (ttmm) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0917 time to fit residues: 5.0530 Evaluate side-chains 44 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.156893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140160 restraints weight = 4285.395| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.00 r_work: 0.3558 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3112 Z= 0.172 Angle : 0.619 6.972 4264 Z= 0.314 Chirality : 0.048 0.230 446 Planarity : 0.004 0.045 556 Dihedral : 4.947 52.073 508 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.91 % Favored : 95.84 % Rotamer: Outliers : 3.14 % Allowed : 13.45 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.41), residues: 409 helix: -3.66 (0.78), residues: 14 sheet: 1.25 (0.41), residues: 149 loop : -0.10 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 346 TYR 0.031 0.002 TYR H 35 PHE 0.012 0.002 PHE R 400 TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3104) covalent geometry : angle 0.60792 ( 4246) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.91752 ( 12) hydrogen bonds : bond 0.02930 ( 100) hydrogen bonds : angle 5.66819 ( 273) link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 1.75922 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.121 Fit side-chains REVERT: L 52 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8012 (t70) REVERT: L 84 ASP cc_start: 0.8333 (m-30) cc_final: 0.8103 (m-30) REVERT: R 462 LYS cc_start: 0.8189 (mttt) cc_final: 0.7939 (ttmm) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.0909 time to fit residues: 4.3805 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138725 restraints weight = 4342.026| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.98 r_work: 0.3538 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3112 Z= 0.212 Angle : 0.662 7.002 4264 Z= 0.338 Chirality : 0.048 0.237 446 Planarity : 0.004 0.046 556 Dihedral : 5.178 51.171 508 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.91 % Favored : 95.84 % Rotamer: Outliers : 2.69 % Allowed : 13.45 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.29 (0.41), residues: 409 helix: -3.68 (0.80), residues: 14 sheet: 1.32 (0.41), residues: 143 loop : -0.23 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 346 TYR 0.039 0.002 TYR H 35 PHE 0.012 0.002 PHE R 400 TRP 0.013 0.001 TRP H 47 HIS 0.001 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 3104) covalent geometry : angle 0.64450 ( 4246) SS BOND : bond 0.00588 ( 6) SS BOND : angle 2.63039 ( 12) hydrogen bonds : bond 0.03160 ( 100) hydrogen bonds : angle 5.84890 ( 273) link_NAG-ASN : bond 0.00144 ( 2) link_NAG-ASN : angle 1.90456 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.075 Fit side-chains REVERT: H 87 ARG cc_start: 0.4480 (tpt170) cc_final: 0.4138 (tpt170) REVERT: L 52 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7987 (t70) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.0932 time to fit residues: 4.2629 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140082 restraints weight = 4294.834| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.97 r_work: 0.3561 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3112 Z= 0.175 Angle : 0.646 6.799 4264 Z= 0.332 Chirality : 0.048 0.232 446 Planarity : 0.004 0.046 556 Dihedral : 5.134 49.770 508 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.16 % Favored : 95.60 % Rotamer: Outliers : 2.24 % Allowed : 15.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.14 (0.41), residues: 409 helix: -3.72 (0.77), residues: 14 sheet: 1.21 (0.41), residues: 138 loop : -0.30 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 346 TYR 0.041 0.002 TYR H 35 PHE 0.012 0.002 PHE R 400 TRP 0.013 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3104) covalent geometry : angle 0.62887 ( 4246) SS BOND : bond 0.00468 ( 6) SS BOND : angle 2.58529 ( 12) hydrogen bonds : bond 0.02934 ( 100) hydrogen bonds : angle 5.98246 ( 273) link_NAG-ASN : bond 0.00130 ( 2) link_NAG-ASN : angle 1.80813 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.115 Fit side-chains REVERT: H 87 ARG cc_start: 0.4542 (tpt170) cc_final: 0.4277 (tpt170) REVERT: L 52 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7784 (t70) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.0970 time to fit residues: 4.2304 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 409 GLN Chi-restraints excluded: chain R residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.0000 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141034 restraints weight = 4263.277| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.96 r_work: 0.3576 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 3112 Z= 0.155 Angle : 0.657 12.246 4264 Z= 0.337 Chirality : 0.048 0.225 446 Planarity : 0.004 0.046 556 Dihedral : 4.970 48.364 508 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.42 % Favored : 96.33 % Rotamer: Outliers : 2.69 % Allowed : 15.25 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.12 (0.41), residues: 409 helix: -3.73 (0.76), residues: 14 sheet: 1.10 (0.41), residues: 144 loop : -0.28 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 346 TYR 0.037 0.002 TYR H 35 PHE 0.013 0.001 PHE R 400 TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3104) covalent geometry : angle 0.63301 ( 4246) SS BOND : bond 0.00887 ( 6) SS BOND : angle 3.16299 ( 12) hydrogen bonds : bond 0.02746 ( 100) hydrogen bonds : angle 5.91458 ( 273) link_NAG-ASN : bond 0.00130 ( 2) link_NAG-ASN : angle 1.67790 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1199.71 seconds wall clock time: 21 minutes 12.15 seconds (1272.15 seconds total)