Starting phenix.real_space_refine on Sat Apr 26 18:25:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asd_43813/04_2025/9asd_43813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asd_43813/04_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_43813/04_2025/9asd_43813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asd_43813/04_2025/9asd_43813.map" model { file = "/net/cci-nas-00/data/ceres_data/9asd_43813/04_2025/9asd_43813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asd_43813/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.38, per 1000 atoms: 1.79 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: 0.73 Conformation dependent library (CDL) restraints added in 404.6 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: 0.48 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: 0.95 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 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: 13.910 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.060 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- 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 : 0.374 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: 0.1870 time to fit residues: 12.3810 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 : 0.325 ------------------------------------------------------------------------------- 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: 0.0020 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: 0.1192 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.171872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159075 restraints weight = 3998.920| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.52 r_work: 0.3850 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3112 Z= 0.101 Angle : 0.572 5.870 4264 Z= 0.303 Chirality : 0.047 0.221 446 Planarity : 0.004 0.030 556 Dihedral : 4.728 50.717 508 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.91 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: -3.55 (1.03), residues: 14 sheet: 0.93 (0.41), residues: 147 loop : 0.27 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.00287 ( 2) link_NAG-ASN : angle 1.31510 ( 6) hydrogen bonds : bond 0.03268 ( 100) hydrogen bonds : angle 6.40977 ( 273) SS BOND : bond 0.00328 ( 6) SS BOND : angle 1.26960 ( 12) covalent geometry : bond 0.00223 ( 3104) covalent geometry : angle 0.56688 ( 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 : 0.326 Fit side-chains revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8757 (m-80) cc_final: 0.8541 (m-80) REVERT: L 52 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7849 (t0) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 0.1898 time to fit residues: 11.2660 Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 0.9990 chunk 38 optimal weight: 0.0470 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 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: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.164450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149885 restraints weight = 4064.777| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.71 r_work: 0.3698 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3112 Z= 0.174 Angle : 0.620 6.764 4264 Z= 0.324 Chirality : 0.049 0.282 446 Planarity : 0.005 0.040 556 Dihedral : 4.959 52.243 508 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.35 % Allowed : 9.42 % Favored : 89.24 % 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: 0.21 (0.40), residues: 409 helix: -3.77 (0.80), residues: 14 sheet: 1.01 (0.40), residues: 151 loop : -0.14 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS R 339 PHE 0.011 0.002 PHE L 48 TYR 0.023 0.002 TYR H 35 ARG 0.002 0.001 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 2) link_NAG-ASN : angle 1.81365 ( 6) hydrogen bonds : bond 0.03314 ( 100) hydrogen bonds : angle 6.02474 ( 273) SS BOND : bond 0.00494 ( 6) SS BOND : angle 1.76755 ( 12) covalent geometry : bond 0.00413 ( 3104) covalent geometry : angle 0.61025 ( 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 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7977 (t70) REVERT: L 84 ASP cc_start: 0.8331 (m-30) cc_final: 0.8109 (m-30) REVERT: R 466 ARG cc_start: 0.8489 (ttp-170) cc_final: 0.8154 (ttp-170) REVERT: R 501 TYR cc_start: 0.6969 (m-10) cc_final: 0.6609 (m-10) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1738 time to fit residues: 9.1828 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 0.2980 chunk 16 optimal weight: 0.0670 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.164768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150041 restraints weight = 4099.548| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.73 r_work: 0.3703 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3112 Z= 0.133 Angle : 0.568 6.791 4264 Z= 0.295 Chirality : 0.048 0.239 446 Planarity : 0.004 0.039 556 Dihedral : 4.796 53.814 508 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 9.87 % 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: 0.33 (0.41), residues: 409 helix: -3.89 (0.71), residues: 14 sheet: 1.19 (0.41), residues: 151 loop : -0.12 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.012 0.001 PHE R 400 TYR 0.030 0.002 TYR H 35 ARG 0.002 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 2) link_NAG-ASN : angle 1.54956 ( 6) hydrogen bonds : bond 0.02912 ( 100) hydrogen bonds : angle 5.74847 ( 273) SS BOND : bond 0.00482 ( 6) SS BOND : angle 1.57076 ( 12) covalent geometry : bond 0.00310 ( 3104) covalent geometry : angle 0.55996 ( 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 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8036 (t70) REVERT: L 84 ASP cc_start: 0.8321 (m-30) cc_final: 0.8089 (m-30) REVERT: R 440 LYS cc_start: 0.9095 (mptt) cc_final: 0.8893 (mptt) REVERT: R 462 LYS cc_start: 0.8256 (mttt) cc_final: 0.8022 (ttmm) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.1819 time to fit residues: 10.1884 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 : 0.300 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.152921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136074 restraints weight = 4313.810| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.00 r_work: 0.3505 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3112 Z= 0.296 Angle : 0.727 7.910 4264 Z= 0.371 Chirality : 0.052 0.274 446 Planarity : 0.005 0.055 556 Dihedral : 5.543 54.685 508 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: 0.11 (0.40), residues: 409 helix: -3.95 (0.74), residues: 14 sheet: 1.19 (0.41), residues: 149 loop : -0.38 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS R 339 PHE 0.014 0.002 PHE L 48 TYR 0.038 0.003 TYR H 35 ARG 0.003 0.001 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 2) link_NAG-ASN : angle 2.27744 ( 6) hydrogen bonds : bond 0.03582 ( 100) hydrogen bonds : angle 6.23585 ( 273) SS BOND : bond 0.00536 ( 6) SS BOND : angle 2.12344 ( 12) covalent geometry : bond 0.00715 ( 3104) covalent geometry : angle 0.71461 ( 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 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8031 (t70) REVERT: R 462 LYS cc_start: 0.8199 (mttt) cc_final: 0.7941 (ttmm) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.1681 time to fit residues: 7.5728 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.0040 overall best weight: 0.2416 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.157241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140682 restraints weight = 4293.721| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.98 r_work: 0.3576 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3623 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= 0.114 Angle : 0.564 6.357 4264 Z= 0.290 Chirality : 0.046 0.221 446 Planarity : 0.004 0.048 556 Dihedral : 4.918 56.074 508 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.79 % Allowed : 12.56 % 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: 0.28 (0.41), residues: 409 helix: -3.99 (0.68), residues: 14 sheet: 1.28 (0.42), residues: 148 loop : -0.23 (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 339 PHE 0.012 0.001 PHE R 400 TYR 0.020 0.001 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 2) link_NAG-ASN : angle 1.57553 ( 6) hydrogen bonds : bond 0.02834 ( 100) hydrogen bonds : angle 5.64494 ( 273) SS BOND : bond 0.00384 ( 6) SS BOND : angle 1.68267 ( 12) covalent geometry : bond 0.00263 ( 3104) covalent geometry : angle 0.55460 ( 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: 4 poor density : 39 time to evaluate : 0.300 Fit side-chains REVERT: L 52 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7990 (t70) REVERT: R 440 LYS cc_start: 0.9179 (mptt) cc_final: 0.8958 (mptt) REVERT: R 462 LYS cc_start: 0.8222 (mttt) cc_final: 0.7964 (ttmm) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.1808 time to fit residues: 9.3380 Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 22 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.155123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138339 restraints weight = 4255.639| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.99 r_work: 0.3540 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3762 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= 0.189 Angle : 0.630 7.032 4264 Z= 0.322 Chirality : 0.048 0.235 446 Planarity : 0.005 0.051 556 Dihedral : 5.141 54.951 508 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % 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: 0.17 (0.41), residues: 409 helix: -3.93 (0.71), residues: 14 sheet: 1.14 (0.42), residues: 149 loop : -0.26 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.001 HIS R 339 PHE 0.011 0.002 PHE R 400 TYR 0.033 0.002 TYR H 35 ARG 0.004 0.001 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 2) link_NAG-ASN : angle 1.86283 ( 6) hydrogen bonds : bond 0.03112 ( 100) hydrogen bonds : angle 5.86080 ( 273) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.92437 ( 12) covalent geometry : bond 0.00454 ( 3104) covalent geometry : angle 0.61878 ( 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 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8089 (t70) REVERT: R 440 LYS cc_start: 0.9188 (mptt) cc_final: 0.8911 (mptt) REVERT: R 462 LYS cc_start: 0.8209 (mttt) cc_final: 0.7947 (ttmm) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.2174 time to fit residues: 10.2064 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.0270 chunk 13 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN L 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141498 restraints weight = 4272.331| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.01 r_work: 0.3569 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3112 Z= 0.121 Angle : 0.571 6.627 4264 Z= 0.295 Chirality : 0.046 0.223 446 Planarity : 0.004 0.049 556 Dihedral : 4.913 55.149 508 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.42 % Favored : 96.33 % Rotamer: Outliers : 1.79 % Allowed : 13.90 % Favored : 84.30 % 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: 0.30 (0.42), residues: 409 helix: -3.90 (0.71), residues: 14 sheet: 1.35 (0.42), residues: 142 loop : -0.22 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.000 0.000 HIS R 339 PHE 0.012 0.001 PHE R 400 TYR 0.026 0.001 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 2) link_NAG-ASN : angle 1.63675 ( 6) hydrogen bonds : bond 0.02777 ( 100) hydrogen bonds : angle 5.59740 ( 273) SS BOND : bond 0.00402 ( 6) SS BOND : angle 1.72159 ( 12) covalent geometry : bond 0.00285 ( 3104) covalent geometry : angle 0.56106 ( 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 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.328 Fit side-chains REVERT: L 52 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8038 (t70) REVERT: R 440 LYS cc_start: 0.9186 (mptt) cc_final: 0.8966 (mptt) REVERT: R 462 LYS cc_start: 0.8210 (mttt) cc_final: 0.7950 (ttmm) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.2047 time to fit residues: 9.8397 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 : 0.331 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.159118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142320 restraints weight = 4293.748| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.01 r_work: 0.3573 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3112 Z= 0.127 Angle : 0.568 6.718 4264 Z= 0.294 Chirality : 0.046 0.225 446 Planarity : 0.004 0.048 556 Dihedral : 4.858 54.263 508 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.40 % Favored : 95.35 % Rotamer: Outliers : 1.79 % Allowed : 14.35 % 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 (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: 0.29 (0.42), residues: 409 helix: -3.90 (0.70), residues: 14 sheet: 1.35 (0.42), residues: 142 loop : -0.23 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.012 0.001 PHE R 400 TYR 0.029 0.002 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 1.59313 ( 6) hydrogen bonds : bond 0.02751 ( 100) hydrogen bonds : angle 5.53241 ( 273) SS BOND : bond 0.00377 ( 6) SS BOND : angle 1.63508 ( 12) covalent geometry : bond 0.00303 ( 3104) covalent geometry : angle 0.55940 ( 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 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 440 LYS cc_start: 0.9170 (mptt) cc_final: 0.8937 (mptt) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.2048 time to fit residues: 9.5515 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.0170 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.156562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140174 restraints weight = 4191.846| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.95 r_work: 0.3559 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3112 Z= 0.188 Angle : 0.636 7.101 4264 Z= 0.327 Chirality : 0.048 0.234 446 Planarity : 0.004 0.049 556 Dihedral : 5.101 51.890 508 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 2.24 % Allowed : 13.45 % Favored : 84.30 % 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: 0.17 (0.41), residues: 409 helix: -3.87 (0.70), residues: 14 sheet: 1.19 (0.42), residues: 144 loop : -0.28 (0.40), residues: 251 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 0.012 0.002 PHE R 400 TYR 0.036 0.002 TYR H 35 ARG 0.004 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 2) link_NAG-ASN : angle 1.81067 ( 6) hydrogen bonds : bond 0.03001 ( 100) hydrogen bonds : angle 5.92403 ( 273) SS BOND : bond 0.00547 ( 6) SS BOND : angle 2.62606 ( 12) covalent geometry : bond 0.00459 ( 3104) covalent geometry : angle 0.61763 ( 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 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.303 Fit side-chains REVERT: L 52 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8040 (t70) REVERT: R 440 LYS cc_start: 0.9181 (mptt) cc_final: 0.8895 (mptt) REVERT: R 462 LYS cc_start: 0.8181 (mttt) cc_final: 0.7921 (ttmm) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.1961 time to fit residues: 8.9101 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 15 optimal weight: 0.3980 chunk 26 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.158041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141577 restraints weight = 4252.954| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.97 r_work: 0.3575 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3112 Z= 0.150 Angle : 0.618 7.318 4264 Z= 0.319 Chirality : 0.047 0.225 446 Planarity : 0.004 0.047 556 Dihedral : 5.031 51.229 508 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 1.35 % Allowed : 14.35 % Favored : 84.30 % 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: 0.11 (0.41), residues: 409 helix: -3.85 (0.72), residues: 14 sheet: 1.03 (0.41), residues: 148 loop : -0.26 (0.40), 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 0.012 0.001 PHE R 400 TYR 0.029 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 1.67097 ( 6) hydrogen bonds : bond 0.02790 ( 100) hydrogen bonds : angle 6.06271 ( 273) SS BOND : bond 0.00418 ( 6) SS BOND : angle 2.75603 ( 12) covalent geometry : bond 0.00372 ( 3104) covalent geometry : angle 0.59831 ( 4246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.65 seconds wall clock time: 42 minutes 37.49 seconds (2557.49 seconds total)