Starting phenix.real_space_refine on Sat Apr 26 21:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gjn_40095/04_2025/8gjn_40095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gjn_40095/04_2025/8gjn_40095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gjn_40095/04_2025/8gjn_40095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gjn_40095/04_2025/8gjn_40095.map" model { file = "/net/cci-nas-00/data/ceres_data/8gjn_40095/04_2025/8gjn_40095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gjn_40095/04_2025/8gjn_40095.cif" } resolution = 3.6 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= 0.011 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 2102 2.51 5 N 550 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3319 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.63, per 1000 atoms: 1.39 Number of scatterers: 3319 At special positions: 0 Unit cell: (86.625, 54.45, 107.25, 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 652 8.00 N 550 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 108 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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 C 601 " - " ASN C 343 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 379.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 13.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.719A pdb=" N TYR A 51 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 4.450A pdb=" N GLY A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.106A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.074A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.213A pdb=" N GLU A 29 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET A 53 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 69 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP A 55 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26 removed outlier: 4.157A pdb=" N VAL B 39 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.388A pdb=" N TRP B 55 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.87 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 801 1.33 - 1.46: 791 1.46 - 1.58: 1791 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3401 Sorted by residual: bond pdb=" N ILE C 472 " pdb=" CA ILE C 472 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N CYS A 115 " pdb=" CA CYS A 115 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ARG C 457 " pdb=" CA ARG C 457 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.18e-02 7.18e+03 9.94e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.93e+00 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 3361 1.75 - 3.50: 1059 3.50 - 5.25: 180 5.25 - 7.00: 13 7.00 - 8.75: 2 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N PHE C 490 " pdb=" CA PHE C 490 " pdb=" C PHE C 490 " ideal model delta sigma weight residual 109.24 100.49 8.75 1.39e+00 5.18e-01 3.96e+01 angle pdb=" N CYS C 488 " pdb=" CA CYS C 488 " pdb=" C CYS C 488 " ideal model delta sigma weight residual 109.54 101.74 7.80 1.37e+00 5.33e-01 3.25e+01 angle pdb=" N TYR C 489 " pdb=" CA TYR C 489 " pdb=" C TYR C 489 " ideal model delta sigma weight residual 110.43 116.65 -6.22 1.31e+00 5.83e-01 2.25e+01 angle pdb=" C GLY A 27 " pdb=" N PRO A 28 " pdb=" CA PRO A 28 " ideal model delta sigma weight residual 119.90 124.65 -4.75 1.02e+00 9.61e-01 2.16e+01 angle pdb=" C LYS B 80 " pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " ideal model delta sigma weight residual 116.54 111.44 5.10 1.15e+00 7.56e-01 1.97e+01 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1851 17.49 - 34.98: 134 34.98 - 52.47: 21 52.47 - 69.95: 21 69.95 - 87.44: 2 Dihedral angle restraints: 2029 sinusoidal: 809 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" C ASP B 61 " pdb=" N GLY B 62 " pdb=" CA GLY B 62 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER B 97 " pdb=" C SER B 97 " pdb=" N PRO B 98 " pdb=" CA PRO B 98 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N VAL A 112 " pdb=" CA VAL A 112 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 2026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 226 0.060 - 0.120: 168 0.120 - 0.180: 80 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA PHE C 464 " pdb=" N PHE C 464 " pdb=" C PHE C 464 " pdb=" CB PHE C 464 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PRO A 33 " pdb=" N PRO A 33 " pdb=" C PRO A 33 " pdb=" CB PRO A 33 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LEU C 461 " pdb=" N LEU C 461 " pdb=" C LEU C 461 " pdb=" CB LEU C 461 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 493 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " -0.104 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" C7 NAG C 601 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " 0.142 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 380 " -0.094 2.00e-02 2.50e+03 5.01e-02 5.01e+01 pdb=" CG TYR C 380 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 380 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR C 380 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 380 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 380 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR C 380 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 380 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 69 " -0.071 2.00e-02 2.50e+03 4.07e-02 3.31e+01 pdb=" CG TYR B 69 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 69 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR B 69 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 69 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 69 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR B 69 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 69 " -0.063 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1409 2.92 - 3.42: 3062 3.42 - 3.91: 5638 3.91 - 4.41: 6166 4.41 - 4.90: 10475 Nonbonded interactions: 26750 Sorted by model distance: nonbonded pdb=" O TYR B 111 " pdb=" OG1 THR C 478 " model vdw 2.431 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" N ASN C 334 " model vdw 2.451 3.120 nonbonded pdb=" O GLN A 24 " pdb=" N LYS A 42 " model vdw 2.470 3.120 nonbonded pdb=" OH TYR C 453 " pdb=" OE1 GLN C 493 " model vdw 2.482 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.506 3.040 ... (remaining 26745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.500 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.013 0.046 3408 Z= 0.826 Angle : 1.677 18.886 4630 Z= 1.123 Chirality : 0.093 0.300 496 Planarity : 0.013 0.098 595 Dihedral : 14.166 87.440 1237 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.10 % Allowed : 7.40 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.73 (0.37), residues: 415 helix: -3.89 (0.58), residues: 26 sheet: -1.56 (0.46), residues: 116 loop : -1.77 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.062 0.008 PHE C 464 TYR 0.094 0.014 TYR C 380 ARG 0.009 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 1) link_NAG-ASN : angle 12.49374 ( 3) hydrogen bonds : bond 0.20146 ( 103) hydrogen bonds : angle 10.18995 ( 249) SS BOND : bond 0.00970 ( 6) SS BOND : angle 1.34600 ( 12) covalent geometry : bond 0.01277 ( 3401) covalent geometry : angle 1.64806 ( 4615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.7469 (tttt) cc_final: 0.7225 (tttt) REVERT: C 367 VAL cc_start: 0.8406 (t) cc_final: 0.8095 (p) outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 0.1513 time to fit residues: 13.1003 Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 12 optimal weight: 0.0010 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 62 GLN B 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.164977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137900 restraints weight = 5802.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142069 restraints weight = 3015.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144775 restraints weight = 1844.481| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3408 Z= 0.140 Angle : 0.601 8.968 4630 Z= 0.314 Chirality : 0.043 0.196 496 Planarity : 0.004 0.032 595 Dihedral : 5.291 35.193 488 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 10.68 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.85 (0.39), residues: 415 helix: -3.79 (0.62), residues: 27 sheet: -1.23 (0.45), residues: 133 loop : -0.87 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.016 0.002 PHE C 497 TYR 0.017 0.002 TYR C 380 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 1) link_NAG-ASN : angle 2.35091 ( 3) hydrogen bonds : bond 0.03816 ( 103) hydrogen bonds : angle 7.69064 ( 249) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.91451 ( 12) covalent geometry : bond 0.00305 ( 3401) covalent geometry : angle 0.59747 ( 4615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7140 (tttt) cc_final: 0.6866 (tttt) REVERT: B 83 SER cc_start: 0.6890 (p) cc_final: 0.6667 (p) REVERT: C 354 ASN cc_start: 0.8139 (m-40) cc_final: 0.7887 (m110) REVERT: C 423 TYR cc_start: 0.8263 (t80) cc_final: 0.8045 (t80) REVERT: C 492 LEU cc_start: 0.8414 (mp) cc_final: 0.8184 (mp) REVERT: C 508 TYR cc_start: 0.8626 (m-10) cc_final: 0.8357 (m-10) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1261 time to fit residues: 12.0666 Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 32 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 57 GLN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.138054 restraints weight = 5836.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142171 restraints weight = 3126.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144715 restraints weight = 1963.085| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3408 Z= 0.112 Angle : 0.531 7.419 4630 Z= 0.275 Chirality : 0.042 0.205 496 Planarity : 0.004 0.038 595 Dihedral : 4.640 34.050 488 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 14.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.49 (0.39), residues: 415 helix: -3.11 (0.78), residues: 27 sheet: -1.00 (0.44), residues: 139 loop : -0.64 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.011 0.001 PHE C 497 TYR 0.011 0.001 TYR C 380 ARG 0.002 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.79585 ( 3) hydrogen bonds : bond 0.03291 ( 103) hydrogen bonds : angle 7.12492 ( 249) SS BOND : bond 0.00233 ( 6) SS BOND : angle 0.73070 ( 12) covalent geometry : bond 0.00236 ( 3401) covalent geometry : angle 0.52840 ( 4615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 367 VAL cc_start: 0.8405 (t) cc_final: 0.8205 (p) REVERT: C 423 TYR cc_start: 0.8367 (t80) cc_final: 0.8162 (t80) REVERT: C 438 SER cc_start: 0.8642 (m) cc_final: 0.8043 (p) REVERT: C 506 GLN cc_start: 0.7954 (mt0) cc_final: 0.7668 (mt0) REVERT: C 508 TYR cc_start: 0.8625 (m-10) cc_final: 0.8354 (m-10) REVERT: C 514 SER cc_start: 0.8509 (t) cc_final: 0.8190 (p) outliers start: 6 outliers final: 5 residues processed: 83 average time/residue: 0.1052 time to fit residues: 11.5748 Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.3980 chunk 11 optimal weight: 0.0060 chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.165441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138416 restraints weight = 5898.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.142593 restraints weight = 3060.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145205 restraints weight = 1883.657| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3408 Z= 0.114 Angle : 0.533 10.325 4630 Z= 0.266 Chirality : 0.042 0.206 496 Planarity : 0.004 0.038 595 Dihedral : 4.532 34.407 488 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.64 % Allowed : 15.34 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.41 (0.39), residues: 415 helix: -2.87 (0.74), residues: 33 sheet: -0.60 (0.44), residues: 140 loop : -0.79 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.008 0.001 PHE C 486 TYR 0.012 0.001 TYR C 380 ARG 0.002 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.48191 ( 3) hydrogen bonds : bond 0.02973 ( 103) hydrogen bonds : angle 6.94075 ( 249) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.61646 ( 12) covalent geometry : bond 0.00251 ( 3401) covalent geometry : angle 0.53151 ( 4615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 478 THR cc_start: 0.8147 (m) cc_final: 0.7805 (p) REVERT: C 508 TYR cc_start: 0.8634 (m-10) cc_final: 0.8411 (m-10) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.1160 time to fit residues: 11.4889 Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN C 354 ASN C 360 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.160034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133447 restraints weight = 5777.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137682 restraints weight = 3040.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140306 restraints weight = 1883.632| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 3408 Z= 0.229 Angle : 0.605 7.122 4630 Z= 0.309 Chirality : 0.044 0.232 496 Planarity : 0.004 0.038 595 Dihedral : 5.203 36.662 488 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.47 % Allowed : 17.53 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.65 (0.39), residues: 415 helix: -2.94 (0.75), residues: 34 sheet: -0.79 (0.42), residues: 147 loop : -0.93 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 55 HIS 0.001 0.000 HIS C 519 PHE 0.010 0.002 PHE C 400 TYR 0.020 0.002 TYR C 423 ARG 0.003 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 1.78060 ( 3) hydrogen bonds : bond 0.03597 ( 103) hydrogen bonds : angle 7.28385 ( 249) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.66005 ( 12) covalent geometry : bond 0.00512 ( 3401) covalent geometry : angle 0.60354 ( 4615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8129 (p-80) REVERT: C 478 THR cc_start: 0.8184 (m) cc_final: 0.7891 (p) REVERT: C 503 VAL cc_start: 0.8438 (t) cc_final: 0.8077 (p) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.1336 time to fit residues: 13.8692 Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.158167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131985 restraints weight = 5893.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136111 restraints weight = 3065.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138717 restraints weight = 1901.193| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3408 Z= 0.223 Angle : 0.612 7.421 4630 Z= 0.312 Chirality : 0.044 0.233 496 Planarity : 0.004 0.040 595 Dihedral : 5.364 34.526 488 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.11 % Allowed : 17.81 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.79 (0.39), residues: 415 helix: -3.11 (0.74), residues: 34 sheet: -0.92 (0.42), residues: 148 loop : -0.99 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.011 0.001 PHE C 400 TYR 0.021 0.002 TYR C 423 ARG 0.002 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 1.50988 ( 3) hydrogen bonds : bond 0.03518 ( 103) hydrogen bonds : angle 7.44157 ( 249) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.88702 ( 12) covalent geometry : bond 0.00500 ( 3401) covalent geometry : angle 0.60985 ( 4615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.8214 (p-80) REVERT: C 478 THR cc_start: 0.8129 (m) cc_final: 0.7842 (p) REVERT: C 487 ASN cc_start: 0.8036 (m-40) cc_final: 0.7760 (m110) outliers start: 15 outliers final: 12 residues processed: 76 average time/residue: 0.1240 time to fit residues: 12.0692 Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 18 optimal weight: 0.0370 chunk 36 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 overall best weight: 0.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135187 restraints weight = 5798.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139348 restraints weight = 3012.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141999 restraints weight = 1857.800| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3408 Z= 0.108 Angle : 0.553 8.121 4630 Z= 0.275 Chirality : 0.043 0.229 496 Planarity : 0.004 0.040 595 Dihedral : 4.685 32.442 488 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.47 % Allowed : 21.10 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.60 (0.40), residues: 415 helix: -3.22 (0.68), residues: 34 sheet: -0.79 (0.43), residues: 144 loop : -0.83 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.008 0.001 PHE C 497 TYR 0.017 0.001 TYR C 423 ARG 0.001 0.000 ARG A 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.20094 ( 3) hydrogen bonds : bond 0.02938 ( 103) hydrogen bonds : angle 6.91941 ( 249) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.77800 ( 12) covalent geometry : bond 0.00237 ( 3401) covalent geometry : angle 0.55163 ( 4615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 478 THR cc_start: 0.8079 (m) cc_final: 0.7711 (p) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.1395 time to fit residues: 13.3084 Evaluate side-chains 72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133031 restraints weight = 5774.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137183 restraints weight = 3007.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139875 restraints weight = 1866.596| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3408 Z= 0.166 Angle : 0.596 8.234 4630 Z= 0.299 Chirality : 0.043 0.145 496 Planarity : 0.004 0.038 595 Dihedral : 4.897 33.953 488 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.01 % Allowed : 20.27 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.58 (0.40), residues: 415 helix: -3.12 (0.72), residues: 34 sheet: -0.76 (0.42), residues: 145 loop : -0.84 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 128 HIS 0.001 0.000 HIS A 60 PHE 0.009 0.001 PHE C 497 TYR 0.012 0.001 TYR B 111 ARG 0.001 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 1) link_NAG-ASN : angle 1.55702 ( 3) hydrogen bonds : bond 0.03285 ( 103) hydrogen bonds : angle 7.19823 ( 249) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.72930 ( 12) covalent geometry : bond 0.00369 ( 3401) covalent geometry : angle 0.59496 ( 4615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 116 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6695 (m) REVERT: C 478 THR cc_start: 0.8109 (m) cc_final: 0.7799 (p) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.1328 time to fit residues: 11.3476 Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.157995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132061 restraints weight = 5757.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136234 restraints weight = 3015.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138860 restraints weight = 1867.692| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3408 Z= 0.186 Angle : 0.623 8.684 4630 Z= 0.311 Chirality : 0.045 0.277 496 Planarity : 0.004 0.034 595 Dihedral : 5.096 34.555 488 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.74 % Allowed : 19.73 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.61 (0.40), residues: 415 helix: -3.13 (0.73), residues: 34 sheet: -0.73 (0.42), residues: 143 loop : -0.90 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 353 HIS 0.001 0.000 HIS A 60 PHE 0.009 0.001 PHE C 497 TYR 0.013 0.002 TYR B 111 ARG 0.002 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.76802 ( 3) hydrogen bonds : bond 0.03438 ( 103) hydrogen bonds : angle 7.34466 ( 249) SS BOND : bond 0.00262 ( 6) SS BOND : angle 0.72162 ( 12) covalent geometry : bond 0.00412 ( 3401) covalent geometry : angle 0.62121 ( 4615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7981 (p0) REVERT: C 478 THR cc_start: 0.8080 (m) cc_final: 0.7761 (p) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.1626 time to fit residues: 14.1201 Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 37 optimal weight: 0.1980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.135458 restraints weight = 5755.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139609 restraints weight = 2993.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142197 restraints weight = 1837.634| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3408 Z= 0.117 Angle : 0.584 8.816 4630 Z= 0.289 Chirality : 0.044 0.270 496 Planarity : 0.004 0.034 595 Dihedral : 4.726 32.313 488 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.01 % Allowed : 20.00 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.45 (0.40), residues: 415 helix: -3.08 (0.70), residues: 34 sheet: -0.61 (0.42), residues: 145 loop : -0.78 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 55 HIS 0.000 0.000 HIS A 60 PHE 0.009 0.001 PHE C 497 TYR 0.008 0.001 TYR C 369 ARG 0.002 0.000 ARG A 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 1.30851 ( 3) hydrogen bonds : bond 0.03068 ( 103) hydrogen bonds : angle 6.95576 ( 249) SS BOND : bond 0.00257 ( 6) SS BOND : angle 0.58457 ( 12) covalent geometry : bond 0.00262 ( 3401) covalent geometry : angle 0.58307 ( 4615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7988 (p0) REVERT: C 423 TYR cc_start: 0.8447 (t80) cc_final: 0.8209 (t80) REVERT: C 478 THR cc_start: 0.8040 (m) cc_final: 0.7664 (p) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.1336 time to fit residues: 11.5898 Evaluate side-chains 72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.157327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131533 restraints weight = 5717.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135661 restraints weight = 2990.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138282 restraints weight = 1855.016| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3408 Z= 0.240 Angle : 0.667 9.072 4630 Z= 0.333 Chirality : 0.045 0.153 496 Planarity : 0.005 0.035 595 Dihedral : 5.279 35.190 488 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.29 % Allowed : 19.45 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.52 (0.41), residues: 415 helix: -3.02 (0.78), residues: 34 sheet: -0.60 (0.43), residues: 143 loop : -0.90 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.009 0.002 PHE A 54 TYR 0.019 0.002 TYR B 111 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 1) link_NAG-ASN : angle 2.18728 ( 3) hydrogen bonds : bond 0.03609 ( 103) hydrogen bonds : angle 7.42949 ( 249) SS BOND : bond 0.00277 ( 6) SS BOND : angle 0.73146 ( 12) covalent geometry : bond 0.00530 ( 3401) covalent geometry : angle 0.66514 ( 4615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.26 seconds wall clock time: 32 minutes 58.28 seconds (1978.28 seconds total)