Starting phenix.real_space_refine on Fri May 9 16:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asd_43813/05_2025/9asd_43813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asd_43813/05_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_43813/05_2025/9asd_43813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asd_43813/05_2025/9asd_43813.map" model { file = "/net/cci-nas-00/data/ceres_data/9asd_43813/05_2025/9asd_43813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asd_43813/05_2025/9asd_43813.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASN:plan1': 3, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 4} 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: 4.62, per 1000 atoms: 1.53 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: 0.74 Conformation dependent library (CDL) restraints added in 398.0 milliseconds 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: 0.51 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: 0.86 Time building geometry restraints manager: 0.89 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (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 TRP 0.020 0.004 TRP H 47 HIS 0.001 0.000 HIS L 41 PHE 0.015 0.003 PHE L 48 TYR 0.038 0.005 TYR L 51 ARG 0.006 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.06304 ( 2) link_NAG-ASN : angle 2.31803 ( 6) hydrogen bonds : bond 0.16298 ( 100) hydrogen bonds : angle 9.10659 ( 273) SS BOND : bond 0.13363 ( 6) SS BOND : angle 5.54497 ( 12) covalent geometry : bond 0.01070 ( 3104) covalent geometry : angle 1.50585 ( 4246) *********************** 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 : 0.340 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: 0.1847 time to fit residues: 12.1947 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 : 0.344 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.2980 chunk 31 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 overall best weight: 0.1222 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.175012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160864 restraints weight = 4084.254| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.70 r_work: 0.3831 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3112 Z= 0.101 Angle : 0.573 5.850 4264 Z= 0.303 Chirality : 0.047 0.225 446 Planarity : 0.004 0.030 556 Dihedral : 4.733 50.831 508 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.69 % Allowed : 5.38 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.41), residues: 409 helix: -3.56 (1.02), residues: 14 sheet: 0.93 (0.40), residues: 147 loop : 0.27 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.001 0.000 HIS L 41 PHE 0.013 0.002 PHE R 377 TYR 0.023 0.002 TYR H 35 ARG 0.003 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 2) link_NAG-ASN : angle 1.31759 ( 6) hydrogen bonds : bond 0.03249 ( 100) hydrogen bonds : angle 6.42639 ( 273) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.24200 ( 12) covalent geometry : bond 0.00223 ( 3104) covalent geometry : angle 0.56783 ( 4246) *********************** 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 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8766 (m-80) cc_final: 0.8550 (m-80) REVERT: L 52 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7880 (t0) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 0.1913 time to fit residues: 11.3505 Evaluate side-chains 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.0070 chunk 38 optimal weight: 0.0010 chunk 7 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.3204 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.164983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151828 restraints weight = 3969.702| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.54 r_work: 0.3738 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3112 Z= 0.141 Angle : 0.576 6.681 4264 Z= 0.301 Chirality : 0.047 0.269 446 Planarity : 0.004 0.036 556 Dihedral : 4.721 52.001 508 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.35 % Allowed : 8.97 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.40), residues: 409 helix: -3.68 (0.85), residues: 14 sheet: 1.08 (0.41), residues: 145 loop : 0.02 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.010 0.002 PHE R 400 TYR 0.022 0.002 TYR H 35 ARG 0.003 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 2) link_NAG-ASN : angle 1.56348 ( 6) hydrogen bonds : bond 0.03140 ( 100) hydrogen bonds : angle 5.94665 ( 273) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.64432 ( 12) covalent geometry : bond 0.00332 ( 3104) covalent geometry : angle 0.56720 ( 4246) *********************** 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 46 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7965 (t70) REVERT: R 501 TYR cc_start: 0.6777 (m-10) cc_final: 0.6514 (m-10) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1686 time to fit residues: 9.4042 Evaluate side-chains 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.0000 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 overall best weight: 0.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155281 restraints weight = 4123.598| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.72 r_work: 0.3755 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2951 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= 0.098 Angle : 0.532 6.536 4264 Z= 0.276 Chirality : 0.047 0.233 446 Planarity : 0.004 0.033 556 Dihedral : 4.580 53.358 508 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.79 % Allowed : 10.31 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.41), residues: 409 helix: -3.80 (0.76), residues: 14 sheet: 1.16 (0.41), residues: 151 loop : 0.08 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.011 0.001 PHE R 400 TYR 0.029 0.001 TYR H 35 ARG 0.002 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 2) link_NAG-ASN : angle 1.32337 ( 6) hydrogen bonds : bond 0.02710 ( 100) hydrogen bonds : angle 5.59822 ( 273) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.37671 ( 12) covalent geometry : bond 0.00217 ( 3104) covalent geometry : angle 0.52552 ( 4246) *********************** 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 49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7965 (t70) REVERT: R 462 LYS cc_start: 0.8212 (mttt) cc_final: 0.7970 (ttmm) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1744 time to fit residues: 10.1359 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET 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 24 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.156182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139330 restraints weight = 4280.722| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.01 r_work: 0.3550 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3112 Z= 0.209 Angle : 0.654 7.438 4264 Z= 0.334 Chirality : 0.050 0.272 446 Planarity : 0.005 0.044 556 Dihedral : 5.121 53.486 508 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.69 % Allowed : 10.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.41), residues: 409 helix: -3.72 (0.79), residues: 14 sheet: 1.30 (0.42), residues: 149 loop : -0.16 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.011 0.002 PHE L 48 TYR 0.034 0.002 TYR H 35 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 2) link_NAG-ASN : angle 1.96964 ( 6) hydrogen bonds : bond 0.03210 ( 100) hydrogen bonds : angle 5.96354 ( 273) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.98499 ( 12) covalent geometry : bond 0.00500 ( 3104) covalent geometry : angle 0.64297 ( 4246) *********************** 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 45 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.317 Fit side-chains REVERT: L 52 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8075 (t70) REVERT: R 462 LYS cc_start: 0.8206 (mttt) cc_final: 0.7954 (ttmm) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.1870 time to fit residues: 9.6255 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.157774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140951 restraints weight = 4308.663| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.01 r_work: 0.3567 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3112 Z= 0.160 Angle : 0.606 7.219 4264 Z= 0.309 Chirality : 0.048 0.230 446 Planarity : 0.004 0.043 556 Dihedral : 4.976 54.162 508 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.24 % Allowed : 12.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.41), residues: 409 helix: -3.88 (0.69), residues: 14 sheet: 1.30 (0.41), residues: 149 loop : -0.15 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.012 0.001 PHE R 400 TYR 0.025 0.002 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 1.70571 ( 6) hydrogen bonds : bond 0.02970 ( 100) hydrogen bonds : angle 5.76335 ( 273) SS BOND : bond 0.00399 ( 6) SS BOND : angle 1.74079 ( 12) covalent geometry : bond 0.00382 ( 3104) covalent geometry : angle 0.59683 ( 4246) *********************** 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 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.319 Fit side-chains REVERT: L 52 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8083 (t70) REVERT: R 440 LYS cc_start: 0.9135 (mptt) cc_final: 0.8881 (mptt) REVERT: R 462 LYS cc_start: 0.8162 (mttt) cc_final: 0.7911 (ttmm) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1917 time to fit residues: 9.5636 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 : 0.315 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 22 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.157735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141139 restraints weight = 4254.172| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.98 r_work: 0.3564 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3112 Z= 0.152 Angle : 0.593 7.246 4264 Z= 0.305 Chirality : 0.047 0.230 446 Planarity : 0.004 0.044 556 Dihedral : 4.962 54.136 508 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 13.00 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.41), residues: 409 helix: -3.92 (0.68), residues: 14 sheet: 1.26 (0.41), residues: 149 loop : -0.18 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS R 339 PHE 0.011 0.001 PHE R 400 TYR 0.016 0.002 TYR H 50 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 2) link_NAG-ASN : angle 1.71036 ( 6) hydrogen bonds : bond 0.02899 ( 100) hydrogen bonds : angle 5.68092 ( 273) SS BOND : bond 0.00395 ( 6) SS BOND : angle 1.82938 ( 12) covalent geometry : bond 0.00362 ( 3104) covalent geometry : angle 0.58269 ( 4246) *********************** 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 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.356 Fit side-chains REVERT: L 52 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8058 (t70) REVERT: R 440 LYS cc_start: 0.9146 (mptt) cc_final: 0.8900 (mptt) REVERT: R 462 LYS cc_start: 0.8170 (mttt) cc_final: 0.7923 (ttmm) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.1838 time to fit residues: 9.0383 Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.155221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138538 restraints weight = 4282.381| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.97 r_work: 0.3543 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3112 Z= 0.220 Angle : 0.662 7.994 4264 Z= 0.339 Chirality : 0.049 0.243 446 Planarity : 0.005 0.047 556 Dihedral : 5.283 53.349 508 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % Rotamer: Outliers : 2.69 % Allowed : 12.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.41), residues: 409 helix: -3.83 (0.73), residues: 14 sheet: 1.12 (0.41), residues: 149 loop : -0.34 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.011 0.002 PHE L 48 TYR 0.024 0.002 TYR H 35 ARG 0.004 0.001 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 1.99040 ( 6) hydrogen bonds : bond 0.03224 ( 100) hydrogen bonds : angle 5.89027 ( 273) SS BOND : bond 0.00480 ( 6) SS BOND : angle 2.09281 ( 12) covalent geometry : bond 0.00532 ( 3104) covalent geometry : angle 0.65021 ( 4246) *********************** 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 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.343 Fit side-chains REVERT: L 52 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7857 (t70) REVERT: R 440 LYS cc_start: 0.9124 (mptt) cc_final: 0.8887 (mptt) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.2021 time to fit residues: 9.0050 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 : 0.343 ------------------------------------------------------------------------------- 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 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.157161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140529 restraints weight = 4284.624| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.98 r_work: 0.3560 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3112 Z= 0.151 Angle : 0.602 7.659 4264 Z= 0.310 Chirality : 0.047 0.231 446 Planarity : 0.004 0.045 556 Dihedral : 5.055 53.257 508 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 1.79 % Allowed : 13.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.41), residues: 409 helix: -3.90 (0.68), residues: 14 sheet: 1.09 (0.41), residues: 148 loop : -0.26 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.011 0.001 PHE R 400 TYR 0.020 0.002 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 2) link_NAG-ASN : angle 1.77710 ( 6) hydrogen bonds : bond 0.02917 ( 100) hydrogen bonds : angle 5.69304 ( 273) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.84308 ( 12) covalent geometry : bond 0.00362 ( 3104) covalent geometry : angle 0.59122 ( 4246) *********************** 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 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.354 Fit side-chains REVERT: L 52 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7993 (t70) REVERT: R 440 LYS cc_start: 0.9161 (mptt) cc_final: 0.8897 (mptt) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.2102 time to fit residues: 9.5369 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 : 0.338 ------------------------------------------------------------------------------- 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 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 21 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.158195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142462 restraints weight = 4166.731| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.87 r_work: 0.3598 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3112 Z= 0.142 Angle : 0.614 7.723 4264 Z= 0.314 Chirality : 0.047 0.230 446 Planarity : 0.004 0.045 556 Dihedral : 5.015 52.198 508 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.16 % Favored : 95.60 % Rotamer: Outliers : 1.79 % Allowed : 13.45 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.41), residues: 409 helix: -3.94 (0.66), residues: 14 sheet: 1.07 (0.41), residues: 148 loop : -0.23 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.013 0.001 PHE R 400 TYR 0.018 0.001 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 1.69597 ( 6) hydrogen bonds : bond 0.02828 ( 100) hydrogen bonds : angle 5.77249 ( 273) SS BOND : bond 0.00438 ( 6) SS BOND : angle 2.48650 ( 12) covalent geometry : bond 0.00343 ( 3104) covalent geometry : angle 0.59792 ( 4246) ********************** 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 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.351 Fit side-chains REVERT: R 440 LYS cc_start: 0.9159 (mptt) cc_final: 0.8910 (mptt) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.2046 time to fit residues: 10.1870 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.0870 chunk 26 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.156837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142175 restraints weight = 4173.442| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.73 r_work: 0.3623 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3112 Z= 0.144 Angle : 0.623 7.850 4264 Z= 0.318 Chirality : 0.047 0.227 446 Planarity : 0.004 0.045 556 Dihedral : 4.982 50.825 508 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.42 % Favored : 96.33 % Rotamer: Outliers : 1.79 % Allowed : 15.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.41), residues: 409 helix: -3.93 (0.69), residues: 14 sheet: 0.98 (0.41), residues: 148 loop : -0.18 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.013 0.001 PHE R 400 TYR 0.030 0.002 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 1.65304 ( 6) hydrogen bonds : bond 0.02726 ( 100) hydrogen bonds : angle 5.92129 ( 273) SS BOND : bond 0.00394 ( 6) SS BOND : angle 2.57678 ( 12) covalent geometry : bond 0.00358 ( 3104) covalent geometry : angle 0.60585 ( 4246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2299.56 seconds wall clock time: 40 minutes 28.41 seconds (2428.41 seconds total)