Starting phenix.real_space_refine on Fri May 9 16:58:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgr_50418/05_2025/9fgr_50418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgr_50418/05_2025/9fgr_50418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgr_50418/05_2025/9fgr_50418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgr_50418/05_2025/9fgr_50418.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgr_50418/05_2025/9fgr_50418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgr_50418/05_2025/9fgr_50418.cif" } resolution = 4.0 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= -0.003 sd= 0.051 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 14 5.16 5 C 2042 2.51 5 N 537 2.21 5 O 616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3209 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1511 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 1 Chain: "E" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1683 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 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: 3.04, per 1000 atoms: 0.95 Number of scatterers: 3209 At special positions: 0 Unit cell: (82.677, 62.23, 81.788, 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 14 16.00 O 616 8.00 N 537 7.00 C 2042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 397.8 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.3% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.099A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.389A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.963A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.959A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 22 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.649A pdb=" N GLY E 10 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR E 115 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 50 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 58 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.514A pdb=" N THR E 138 " --> pdb=" O ARG E 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 187 through 188 removed outlier: 5.792A pdb=" N LEU E 180 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN E 171 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 182 " --> pdb=" O TRP E 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 188 removed outlier: 5.792A pdb=" N LEU E 180 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN E 171 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 182 " --> pdb=" O TRP E 169 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 213 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: 0.77 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1025 1.35 - 1.47: 884 1.47 - 1.59: 1362 1.59 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3287 Sorted by residual: bond pdb=" CA THR C 470 " pdb=" CB THR C 470 " ideal model delta sigma weight residual 1.528 1.583 -0.055 2.61e-02 1.47e+03 4.40e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C3 NAG C1301 " pdb=" O3 NAG C1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.80e-01 bond pdb=" C2 NAG C1301 " pdb=" N2 NAG C1301 " ideal model delta sigma weight residual 1.439 1.457 -0.018 2.00e-02 2.50e+03 7.88e-01 ... (remaining 3282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 4282 1.24 - 2.49: 139 2.49 - 3.73: 32 3.73 - 4.98: 8 4.98 - 6.22: 2 Bond angle restraints: 4463 Sorted by residual: angle pdb=" N SER E 140 " pdb=" CA SER E 140 " pdb=" C SER E 140 " ideal model delta sigma weight residual 109.81 116.03 -6.22 2.21e+00 2.05e-01 7.92e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.60 112.37 -3.77 1.46e+00 4.69e-01 6.67e+00 angle pdb=" CA LYS C 386 " pdb=" CB LYS C 386 " pdb=" CG LYS C 386 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.25e+00 angle pdb=" N GLY E 198 " pdb=" CA GLY E 198 " pdb=" C GLY E 198 " ideal model delta sigma weight residual 110.90 114.03 -3.13 1.53e+00 4.27e-01 4.18e+00 angle pdb=" N SER E 35 " pdb=" CA SER E 35 " pdb=" C SER E 35 " ideal model delta sigma weight residual 108.55 111.69 -3.14 1.62e+00 3.81e-01 3.75e+00 ... (remaining 4458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 1748 16.77 - 33.55: 154 33.55 - 50.32: 37 50.32 - 67.09: 3 67.09 - 83.87: 1 Dihedral angle restraints: 1943 sinusoidal: 764 harmonic: 1179 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 142.95 -49.95 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual -86.00 -128.20 42.20 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual -180.00 -156.80 -23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 1940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 327 0.034 - 0.069: 100 0.069 - 0.103: 37 0.103 - 0.137: 16 0.137 - 0.171: 1 Chirality restraints: 481 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA SER E 228 " pdb=" N SER E 228 " pdb=" C SER E 228 " pdb=" CB SER E 228 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE E 182 " pdb=" N ILE E 182 " pdb=" C ILE E 182 " pdb=" CB ILE E 182 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 478 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 147 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 148 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 148 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 148 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 140 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO E 141 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 141 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 141 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 498 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO C 499 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.017 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 126 2.72 - 3.27: 3136 3.27 - 3.81: 4692 3.81 - 4.36: 5568 4.36 - 4.90: 9744 Nonbonded interactions: 23266 Sorted by model distance: nonbonded pdb=" OG SER E 147 " pdb=" OE1 GLU E 150 " model vdw 2.176 3.040 nonbonded pdb=" O ALA C 475 " pdb=" OG1 THR E 28 " model vdw 2.186 3.040 nonbonded pdb=" OG SER E 159 " pdb=" OE1 GLN E 160 " model vdw 2.206 3.040 nonbonded pdb=" O ALA E 104 " pdb=" OH TYR E 170 " model vdw 2.212 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.286 3.040 ... (remaining 23261 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=0.00 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: 2.680 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.003 0.055 3294 Z= 0.120 Angle : 0.592 6.986 4478 Z= 0.311 Chirality : 0.042 0.171 481 Planarity : 0.004 0.036 578 Dihedral : 12.554 83.866 1181 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.53 (0.40), residues: 404 helix: -4.11 (0.47), residues: 20 sheet: 0.12 (0.52), residues: 112 loop : -1.33 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 169 PHE 0.014 0.001 PHE C 429 TYR 0.011 0.001 TYR E 225 ARG 0.002 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 5.16495 ( 3) hydrogen bonds : bond 0.29890 ( 79) hydrogen bonds : angle 10.79930 ( 213) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.78810 ( 12) covalent geometry : bond 0.00251 ( 3287) covalent geometry : angle 0.57633 ( 4463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: E 89 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (m-30) REVERT: E 238 ARG cc_start: 0.7467 (pmt170) cc_final: 0.6991 (ptp90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1758 time to fit residues: 16.3781 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115040 restraints weight = 6138.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115223 restraints weight = 4661.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115446 restraints weight = 4408.560| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3294 Z= 0.147 Angle : 0.603 6.247 4478 Z= 0.316 Chirality : 0.044 0.154 481 Planarity : 0.004 0.035 578 Dihedral : 5.656 54.045 476 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.32 % Allowed : 11.59 % Favored : 86.09 % 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: -1.39 (0.39), residues: 404 helix: -3.96 (0.54), residues: 23 sheet: 0.22 (0.46), residues: 123 loop : -1.26 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 PHE 0.014 0.001 PHE E 205 TYR 0.016 0.001 TYR C 473 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 2.67018 ( 3) hydrogen bonds : bond 0.04200 ( 79) hydrogen bonds : angle 7.39279 ( 213) SS BOND : bond 0.00586 ( 6) SS BOND : angle 1.15169 ( 12) covalent geometry : bond 0.00341 ( 3287) covalent geometry : angle 0.59657 ( 4463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.309 Fit side-chains REVERT: C 357 ARG cc_start: 0.7425 (mtp85) cc_final: 0.6315 (mtm180) REVERT: C 406 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7509 (mt-10) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.1586 time to fit residues: 12.6617 Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain E residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105883 restraints weight = 6407.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107872 restraints weight = 4650.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109197 restraints weight = 3726.493| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3294 Z= 0.246 Angle : 0.662 6.464 4478 Z= 0.352 Chirality : 0.045 0.152 481 Planarity : 0.005 0.037 578 Dihedral : 6.162 54.493 476 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.19 % Allowed : 15.07 % Favored : 81.74 % 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: -1.65 (0.39), residues: 404 helix: -4.04 (0.51), residues: 23 sheet: -0.01 (0.45), residues: 133 loop : -1.47 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 436 PHE 0.013 0.002 PHE E 205 TYR 0.018 0.002 TYR C 453 ARG 0.005 0.001 ARG E 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 1.88163 ( 3) hydrogen bonds : bond 0.04413 ( 79) hydrogen bonds : angle 7.06729 ( 213) SS BOND : bond 0.00596 ( 6) SS BOND : angle 1.36407 ( 12) covalent geometry : bond 0.00575 ( 3287) covalent geometry : angle 0.65769 ( 4463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.372 Fit side-chains REVERT: C 378 LYS cc_start: 0.8671 (mttp) cc_final: 0.7971 (mmtm) REVERT: E 88 GLU cc_start: 0.7649 (pp20) cc_final: 0.7314 (pp20) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1715 time to fit residues: 13.6414 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112198 restraints weight = 6040.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113871 restraints weight = 4548.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115134 restraints weight = 3719.245| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3294 Z= 0.142 Angle : 0.582 6.249 4478 Z= 0.307 Chirality : 0.043 0.142 481 Planarity : 0.004 0.037 578 Dihedral : 5.819 54.443 476 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.06 % Allowed : 16.23 % Favored : 79.71 % 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: -1.50 (0.40), residues: 404 helix: -3.84 (0.62), residues: 23 sheet: 0.18 (0.45), residues: 132 loop : -1.43 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 PHE 0.011 0.001 PHE E 155 TYR 0.025 0.001 TYR C 473 ARG 0.002 0.000 ARG E 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 1) link_NAG-ASN : angle 1.49376 ( 3) hydrogen bonds : bond 0.03572 ( 79) hydrogen bonds : angle 6.47295 ( 213) SS BOND : bond 0.00542 ( 6) SS BOND : angle 1.12493 ( 12) covalent geometry : bond 0.00330 ( 3287) covalent geometry : angle 0.57923 ( 4463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.368 Fit side-chains REVERT: C 378 LYS cc_start: 0.8460 (mttp) cc_final: 0.7921 (mmtm) REVERT: E 88 GLU cc_start: 0.7642 (pp20) cc_final: 0.7395 (pp20) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.1673 time to fit residues: 13.1194 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 209 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111274 restraints weight = 6043.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112895 restraints weight = 4595.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113897 restraints weight = 3767.494| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3294 Z= 0.169 Angle : 0.593 6.212 4478 Z= 0.313 Chirality : 0.043 0.140 481 Planarity : 0.004 0.039 578 Dihedral : 5.879 54.516 476 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.06 % Allowed : 17.39 % Favored : 78.55 % 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: -1.50 (0.40), residues: 404 helix: -3.89 (0.61), residues: 23 sheet: 0.27 (0.46), residues: 132 loop : -1.48 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.011 0.001 PHE E 155 TYR 0.012 0.001 TYR C 453 ARG 0.003 0.000 ARG E 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 1.45083 ( 3) hydrogen bonds : bond 0.03603 ( 79) hydrogen bonds : angle 6.38831 ( 213) SS BOND : bond 0.00545 ( 6) SS BOND : angle 1.17462 ( 12) covalent geometry : bond 0.00394 ( 3287) covalent geometry : angle 0.58996 ( 4463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.389 Fit side-chains REVERT: C 378 LYS cc_start: 0.8549 (mttp) cc_final: 0.7944 (mmtm) REVERT: E 88 GLU cc_start: 0.7825 (pp20) cc_final: 0.7510 (pp20) outliers start: 14 outliers final: 11 residues processed: 66 average time/residue: 0.1698 time to fit residues: 13.4610 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN E 73 ASN ** E 139 GLN ** 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 = 0.3526 r_free = 0.3526 target = 0.130606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112690 restraints weight = 6201.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114454 restraints weight = 4544.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115703 restraints weight = 3670.403| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3294 Z= 0.133 Angle : 0.577 6.179 4478 Z= 0.301 Chirality : 0.042 0.137 481 Planarity : 0.004 0.035 578 Dihedral : 5.754 54.523 476 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.64 % Allowed : 17.10 % Favored : 78.26 % 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: -1.41 (0.40), residues: 404 helix: -3.78 (0.67), residues: 23 sheet: 0.43 (0.48), residues: 127 loop : -1.45 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.014 0.001 PHE E 205 TYR 0.009 0.001 TYR C 453 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 1.39307 ( 3) hydrogen bonds : bond 0.03234 ( 79) hydrogen bonds : angle 6.18739 ( 213) SS BOND : bond 0.00527 ( 6) SS BOND : angle 1.08391 ( 12) covalent geometry : bond 0.00310 ( 3287) covalent geometry : angle 0.57448 ( 4463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.376 Fit side-chains REVERT: C 378 LYS cc_start: 0.8511 (mttp) cc_final: 0.7964 (mmtm) REVERT: E 88 GLU cc_start: 0.7863 (pp20) cc_final: 0.7575 (pp20) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.1465 time to fit residues: 12.4686 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 1 optimal weight: 0.0010 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN E 73 ASN ** E 139 GLN ** 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 = 0.3539 r_free = 0.3539 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113396 restraints weight = 6130.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115127 restraints weight = 4517.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116520 restraints weight = 3663.207| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3294 Z= 0.122 Angle : 0.573 6.407 4478 Z= 0.294 Chirality : 0.042 0.133 481 Planarity : 0.004 0.032 578 Dihedral : 5.612 54.187 476 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.77 % Allowed : 18.26 % Favored : 77.97 % 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: -1.29 (0.41), residues: 404 helix: -3.71 (0.71), residues: 23 sheet: 0.63 (0.49), residues: 128 loop : -1.46 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.011 0.001 PHE E 205 TYR 0.010 0.001 TYR E 170 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 1.35334 ( 3) hydrogen bonds : bond 0.03040 ( 79) hydrogen bonds : angle 5.96387 ( 213) SS BOND : bond 0.00508 ( 6) SS BOND : angle 1.01066 ( 12) covalent geometry : bond 0.00283 ( 3287) covalent geometry : angle 0.57064 ( 4463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.392 Fit side-chains REVERT: C 338 PHE cc_start: 0.6945 (p90) cc_final: 0.6679 (p90) REVERT: C 378 LYS cc_start: 0.8508 (mttp) cc_final: 0.7913 (mmtm) REVERT: E 88 GLU cc_start: 0.7862 (pp20) cc_final: 0.7566 (pp20) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.1582 time to fit residues: 12.3115 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 15 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115097 restraints weight = 6121.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116984 restraints weight = 4462.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118245 restraints weight = 3568.179| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3294 Z= 0.113 Angle : 0.571 6.444 4478 Z= 0.294 Chirality : 0.042 0.134 481 Planarity : 0.004 0.034 578 Dihedral : 5.534 54.247 476 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.48 % Allowed : 20.58 % Favored : 75.94 % 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: -1.23 (0.41), residues: 404 helix: -3.66 (0.73), residues: 23 sheet: 0.73 (0.49), residues: 128 loop : -1.45 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.010 0.001 PHE E 205 TYR 0.011 0.001 TYR E 170 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 1.43739 ( 3) hydrogen bonds : bond 0.02867 ( 79) hydrogen bonds : angle 5.85521 ( 213) SS BOND : bond 0.00469 ( 6) SS BOND : angle 0.94364 ( 12) covalent geometry : bond 0.00261 ( 3287) covalent geometry : angle 0.56869 ( 4463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8464 (mttp) cc_final: 0.7870 (mmtm) REVERT: E 88 GLU cc_start: 0.7877 (pp20) cc_final: 0.7553 (pp20) REVERT: E 224 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8052 (tm-30) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.1515 time to fit residues: 11.9910 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111239 restraints weight = 6107.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113091 restraints weight = 4494.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114282 restraints weight = 3635.698| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3294 Z= 0.163 Angle : 0.617 7.521 4478 Z= 0.317 Chirality : 0.044 0.144 481 Planarity : 0.004 0.034 578 Dihedral : 5.759 54.310 476 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.48 % Allowed : 19.71 % Favored : 76.81 % 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: -1.30 (0.41), residues: 404 helix: -3.75 (0.67), residues: 23 sheet: 0.57 (0.49), residues: 127 loop : -1.41 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.014 0.001 PHE E 205 TYR 0.015 0.001 TYR E 52 ARG 0.003 0.000 ARG E 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.73804 ( 3) hydrogen bonds : bond 0.03224 ( 79) hydrogen bonds : angle 6.02055 ( 213) SS BOND : bond 0.00489 ( 6) SS BOND : angle 0.97828 ( 12) covalent geometry : bond 0.00383 ( 3287) covalent geometry : angle 0.61470 ( 4463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.352 Fit side-chains REVERT: C 338 PHE cc_start: 0.7038 (p90) cc_final: 0.6663 (p90) REVERT: C 378 LYS cc_start: 0.8503 (mttp) cc_final: 0.7909 (mmtm) REVERT: E 88 GLU cc_start: 0.7955 (pp20) cc_final: 0.7558 (pp20) REVERT: E 205 PHE cc_start: 0.8266 (m-10) cc_final: 0.7987 (m-10) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.1498 time to fit residues: 11.8075 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113394 restraints weight = 6053.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115103 restraints weight = 4499.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116498 restraints weight = 3673.312| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3294 Z= 0.137 Angle : 0.607 7.127 4478 Z= 0.314 Chirality : 0.043 0.141 481 Planarity : 0.004 0.034 578 Dihedral : 5.697 53.846 476 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.48 % Allowed : 20.58 % Favored : 75.94 % 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: -1.30 (0.41), residues: 404 helix: -3.71 (0.69), residues: 23 sheet: 0.56 (0.48), residues: 133 loop : -1.46 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.015 0.001 PHE E 205 TYR 0.015 0.001 TYR E 170 ARG 0.004 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 1.79332 ( 3) hydrogen bonds : bond 0.03023 ( 79) hydrogen bonds : angle 5.96073 ( 213) SS BOND : bond 0.00491 ( 6) SS BOND : angle 0.91228 ( 12) covalent geometry : bond 0.00322 ( 3287) covalent geometry : angle 0.60406 ( 4463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.385 Fit side-chains REVERT: C 338 PHE cc_start: 0.7026 (p90) cc_final: 0.6617 (p90) REVERT: C 378 LYS cc_start: 0.8474 (mttp) cc_final: 0.7886 (mmtm) REVERT: E 88 GLU cc_start: 0.7935 (pp20) cc_final: 0.7537 (pp20) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.1313 time to fit residues: 10.3276 Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116250 restraints weight = 5988.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116759 restraints weight = 4453.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117814 restraints weight = 4665.783| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3294 Z= 0.134 Angle : 0.606 7.224 4478 Z= 0.312 Chirality : 0.043 0.139 481 Planarity : 0.004 0.034 578 Dihedral : 5.616 53.329 476 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.90 % Allowed : 21.16 % Favored : 75.94 % 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: -1.34 (0.41), residues: 404 helix: -3.66 (0.72), residues: 23 sheet: 0.57 (0.49), residues: 128 loop : -1.48 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.022 0.001 PHE E 205 TYR 0.015 0.001 TYR E 170 ARG 0.003 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 1.92882 ( 3) hydrogen bonds : bond 0.03005 ( 79) hydrogen bonds : angle 5.87542 ( 213) SS BOND : bond 0.00499 ( 6) SS BOND : angle 0.92020 ( 12) covalent geometry : bond 0.00311 ( 3287) covalent geometry : angle 0.60271 ( 4463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1447.49 seconds wall clock time: 26 minutes 17.65 seconds (1577.65 seconds total)