Starting phenix.real_space_refine on Sat Apr 26 18:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgt_50424/04_2025/9fgt_50424.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgt_50424/04_2025/9fgt_50424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgt_50424/04_2025/9fgt_50424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgt_50424/04_2025/9fgt_50424.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgt_50424/04_2025/9fgt_50424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgt_50424/04_2025/9fgt_50424.cif" } resolution = 3.8 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= -0.006 sd= 0.052 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 10 5.16 5 C 1863 2.51 5 N 496 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 2921 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 2 Chain: "E" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 2 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: 2.99, per 1000 atoms: 1.02 Number of scatterers: 2921 At special positions: 0 Unit cell: (78.232, 65.786, 79.121, 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 10 16.00 O 552 8.00 N 496 7.00 C 1863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " 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: 0.70 Conformation dependent library (CDL) restraints added in 367.7 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 8.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.523A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.211A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.589A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.884A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.586A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.761A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 18 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.921A pdb=" N ALA E 96 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.668A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 172 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.668A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 172 " --> pdb=" O VAL E 219 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 183 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: 0.70 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 925 1.34 - 1.46: 657 1.46 - 1.57: 1399 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2993 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.446 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CA VAL C 395 " pdb=" C VAL C 395 " ideal model delta sigma weight residual 1.525 1.502 0.023 2.10e-02 2.27e+03 1.21e+00 bond pdb=" C SER E 100 " pdb=" O SER E 100 " ideal model delta sigma weight residual 1.235 1.222 0.013 1.26e-02 6.30e+03 1.12e+00 bond pdb=" CB TRP E 47 " pdb=" CG TRP E 47 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.04e+00 ... (remaining 2988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 3878 1.51 - 3.03: 150 3.03 - 4.54: 21 4.54 - 6.05: 8 6.05 - 7.56: 1 Bond angle restraints: 4058 Sorted by residual: angle pdb=" C ASN C 343 " pdb=" CA ASN C 343 " pdb=" CB ASN C 343 " ideal model delta sigma weight residual 109.80 115.12 -5.32 1.70e+00 3.46e-01 9.80e+00 angle pdb=" C PRO C 479 " pdb=" N CYS C 480 " pdb=" CA CYS C 480 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.18e+00 angle pdb=" C LEU E 99 " pdb=" N SER E 100 " pdb=" CA SER E 100 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.98e+00 angle pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C5 NAG C1301 " ideal model delta sigma weight residual 113.21 120.77 -7.56 3.00e+00 1.11e-01 6.36e+00 angle pdb=" CA ASP C 428 " pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.05e+00 ... (remaining 4053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 1640 22.35 - 44.69: 96 44.69 - 67.04: 21 67.04 - 89.39: 0 89.39 - 111.73: 3 Dihedral angle restraints: 1760 sinusoidal: 691 harmonic: 1069 Sorted by residual: dihedral pdb=" CB CYS E 156 " pdb=" SG CYS E 156 " pdb=" SG CYS E 222 " pdb=" CB CYS E 222 " ideal model delta sinusoidal sigma weight residual 93.00 145.53 -52.53 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" C1 NAG C1301 " pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C4 NAG C1301 " ideal model delta sinusoidal sigma weight residual -64.11 47.62 -111.73 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 NAG C1301 " pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C6 NAG C1301 " ideal model delta sinusoidal sigma weight residual 171.16 -78.54 -110.30 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 1757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 319 0.047 - 0.094: 84 0.094 - 0.141: 29 0.141 - 0.188: 1 0.188 - 0.236: 2 Chirality restraints: 435 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 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU E 167 " pdb=" CB LEU E 167 " pdb=" CD1 LEU E 167 " pdb=" CD2 LEU E 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 432 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 13 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO E 14 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 225 " -0.012 2.00e-02 2.50e+03 1.31e-02 3.44e+00 pdb=" CG TYR E 225 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 225 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 225 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 225 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 225 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 225 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " 0.016 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 453 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " 0.002 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 44 2.66 - 3.22: 2668 3.22 - 3.78: 3965 3.78 - 4.34: 5381 4.34 - 4.90: 9059 Nonbonded interactions: 21117 Sorted by model distance: nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.094 3.040 nonbonded pdb=" O GLY E 142 " pdb=" OG1 THR E 236 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 376 " pdb=" O ALA C 435 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 473 " pdb=" O ALA E 31 " model vdw 2.303 3.040 nonbonded pdb=" NH1 ARG E 188 " pdb=" O PHE E 196 " model vdw 2.315 3.120 ... (remaining 21112 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: 2.660 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.005 0.081 2998 Z= 0.238 Angle : 0.709 7.564 4069 Z= 0.371 Chirality : 0.049 0.236 435 Planarity : 0.005 0.050 521 Dihedral : 14.859 111.732 1072 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.56 (0.43), residues: 361 helix: -3.41 (1.05), residues: 13 sheet: -0.18 (0.51), residues: 117 loop : -1.41 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.017 0.002 PHE E 205 TYR 0.029 0.002 TYR E 225 ARG 0.004 0.001 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.01418 ( 1) link_NAG-ASN : angle 3.23295 ( 3) hydrogen bonds : bond 0.30511 ( 70) hydrogen bonds : angle 10.49492 ( 183) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.08017 ( 8) covalent geometry : bond 0.00540 ( 2993) covalent geometry : angle 0.70291 ( 4058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.298 Fit side-chains REVERT: C 458 LYS cc_start: 0.8502 (mttt) cc_final: 0.8291 (mttp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1128 time to fit residues: 7.9634 Evaluate side-chains 49 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 0.0470 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130942 restraints weight = 5126.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133962 restraints weight = 3053.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136152 restraints weight = 2103.421| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2998 Z= 0.141 Angle : 0.683 12.814 4069 Z= 0.339 Chirality : 0.046 0.140 435 Planarity : 0.005 0.052 521 Dihedral : 8.790 69.202 436 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.93 % Allowed : 10.29 % Favored : 87.78 % 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: -1.42 (0.43), residues: 361 helix: -3.21 (1.17), residues: 13 sheet: 0.03 (0.53), residues: 110 loop : -1.35 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.009 0.001 PHE E 205 TYR 0.016 0.001 TYR E 225 ARG 0.002 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.01459 ( 1) link_NAG-ASN : angle 2.76078 ( 3) hydrogen bonds : bond 0.05078 ( 70) hydrogen bonds : angle 7.12550 ( 183) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.90564 ( 8) covalent geometry : bond 0.00320 ( 2993) covalent geometry : angle 0.67858 ( 4058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.352 Fit side-chains REVERT: C 406 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7671 (mt-10) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.1256 time to fit residues: 9.3357 Evaluate side-chains 58 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3728 r_free = 0.3728 target = 0.148002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128129 restraints weight = 5106.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131094 restraints weight = 3097.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133077 restraints weight = 2151.434| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2998 Z= 0.187 Angle : 0.652 7.462 4069 Z= 0.333 Chirality : 0.046 0.188 435 Planarity : 0.005 0.052 521 Dihedral : 7.125 59.855 436 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.57 % Allowed : 13.83 % Favored : 83.60 % 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: -1.62 (0.43), residues: 361 helix: -3.36 (1.11), residues: 13 sheet: -0.07 (0.54), residues: 110 loop : -1.51 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.020 0.002 PHE C 486 TYR 0.016 0.002 TYR E 225 ARG 0.003 0.000 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 1) link_NAG-ASN : angle 2.71890 ( 3) hydrogen bonds : bond 0.04684 ( 70) hydrogen bonds : angle 6.56557 ( 183) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.03191 ( 8) covalent geometry : bond 0.00445 ( 2993) covalent geometry : angle 0.64714 ( 4058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.326 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.1114 time to fit residues: 7.7761 Evaluate side-chains 54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 1 optimal weight: 0.0970 chunk 16 optimal weight: 0.0980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3776 r_free = 0.3776 target = 0.151581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131922 restraints weight = 5115.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134949 restraints weight = 3080.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136998 restraints weight = 2127.873| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2998 Z= 0.114 Angle : 0.580 7.378 4069 Z= 0.295 Chirality : 0.044 0.139 435 Planarity : 0.004 0.052 521 Dihedral : 6.464 59.828 436 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.57 % Allowed : 14.47 % Favored : 82.96 % 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: -1.58 (0.43), residues: 361 helix: -2.96 (1.29), residues: 13 sheet: -0.04 (0.54), residues: 110 loop : -1.51 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.006 0.001 PHE E 205 TYR 0.018 0.001 TYR E 225 ARG 0.002 0.000 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 1) link_NAG-ASN : angle 2.12551 ( 3) hydrogen bonds : bond 0.03740 ( 70) hydrogen bonds : angle 6.11793 ( 183) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.68641 ( 8) covalent geometry : bond 0.00267 ( 2993) covalent geometry : angle 0.57740 ( 4058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.269 Fit side-chains REVERT: C 473 TYR cc_start: 0.8242 (t80) cc_final: 0.8030 (t80) REVERT: E 83 ASN cc_start: 0.7945 (m110) cc_final: 0.7565 (m-40) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1196 time to fit residues: 9.6142 Evaluate side-chains 60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.148463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128564 restraints weight = 5140.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131508 restraints weight = 3109.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133634 restraints weight = 2173.874| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2998 Z= 0.166 Angle : 0.626 7.540 4069 Z= 0.319 Chirality : 0.045 0.140 435 Planarity : 0.004 0.052 521 Dihedral : 6.280 54.618 436 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.22 % Allowed : 15.11 % Favored : 81.67 % 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: -1.76 (0.43), residues: 361 helix: -2.84 (1.42), residues: 13 sheet: -0.13 (0.54), residues: 109 loop : -1.67 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 108 HIS 0.001 0.001 HIS C 505 PHE 0.032 0.002 PHE E 205 TYR 0.016 0.001 TYR E 225 ARG 0.002 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 1) link_NAG-ASN : angle 2.56349 ( 3) hydrogen bonds : bond 0.03905 ( 70) hydrogen bonds : angle 6.11295 ( 183) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.85855 ( 8) covalent geometry : bond 0.00398 ( 2993) covalent geometry : angle 0.62154 ( 4058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.328 Fit side-chains REVERT: E 205 PHE cc_start: 0.8607 (m-80) cc_final: 0.8391 (m-10) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.1131 time to fit residues: 8.0700 Evaluate side-chains 55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 31 optimal weight: 0.0870 chunk 5 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3795 r_free = 0.3795 target = 0.153109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133258 restraints weight = 5189.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136407 restraints weight = 3084.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138626 restraints weight = 2108.650| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2998 Z= 0.103 Angle : 0.569 7.458 4069 Z= 0.287 Chirality : 0.044 0.139 435 Planarity : 0.004 0.053 521 Dihedral : 5.524 56.381 436 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 16.40 % Favored : 80.71 % 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: -1.62 (0.43), residues: 361 helix: -2.65 (1.54), residues: 13 sheet: -0.02 (0.55), residues: 108 loop : -1.58 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.028 0.001 PHE C 486 TYR 0.017 0.001 TYR E 225 ARG 0.002 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 1) link_NAG-ASN : angle 1.73616 ( 3) hydrogen bonds : bond 0.03222 ( 70) hydrogen bonds : angle 5.78670 ( 183) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.59169 ( 8) covalent geometry : bond 0.00241 ( 2993) covalent geometry : angle 0.56691 ( 4058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.294 Fit side-chains REVERT: E 83 ASN cc_start: 0.7908 (m110) cc_final: 0.7516 (m-40) REVERT: E 205 PHE cc_start: 0.8567 (m-80) cc_final: 0.8327 (m-10) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.0962 time to fit residues: 7.4910 Evaluate side-chains 57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.151164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131198 restraints weight = 5256.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134283 restraints weight = 3140.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136471 restraints weight = 2163.955| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2998 Z= 0.129 Angle : 0.598 8.149 4069 Z= 0.299 Chirality : 0.045 0.138 435 Planarity : 0.004 0.052 521 Dihedral : 5.494 53.352 436 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.89 % Allowed : 17.68 % Favored : 79.42 % 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: -1.67 (0.43), residues: 361 helix: -2.75 (1.48), residues: 13 sheet: -0.01 (0.55), residues: 107 loop : -1.62 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.027 0.001 PHE E 205 TYR 0.016 0.001 TYR E 225 ARG 0.001 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 1) link_NAG-ASN : angle 1.99914 ( 3) hydrogen bonds : bond 0.03402 ( 70) hydrogen bonds : angle 5.76240 ( 183) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.72359 ( 8) covalent geometry : bond 0.00311 ( 2993) covalent geometry : angle 0.59537 ( 4058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.313 Fit side-chains REVERT: E 83 ASN cc_start: 0.7947 (m110) cc_final: 0.7530 (m-40) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1211 time to fit residues: 8.5411 Evaluate side-chains 57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3767 r_free = 0.3767 target = 0.151174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132305 restraints weight = 5117.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135063 restraints weight = 3151.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137022 restraints weight = 2225.011| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2998 Z= 0.128 Angle : 0.611 8.044 4069 Z= 0.302 Chirality : 0.045 0.139 435 Planarity : 0.004 0.052 521 Dihedral : 5.452 53.169 436 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.89 % Allowed : 18.33 % Favored : 78.78 % 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: -1.68 (0.43), residues: 361 helix: -2.96 (1.32), residues: 13 sheet: 0.01 (0.55), residues: 107 loop : -1.63 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.030 0.001 PHE C 486 TYR 0.016 0.001 TYR E 225 ARG 0.001 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 1.94954 ( 3) hydrogen bonds : bond 0.03407 ( 70) hydrogen bonds : angle 5.77200 ( 183) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.67115 ( 8) covalent geometry : bond 0.00307 ( 2993) covalent geometry : angle 0.60895 ( 4058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.344 Fit side-chains REVERT: E 83 ASN cc_start: 0.7842 (m110) cc_final: 0.7500 (m-40) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.1287 time to fit residues: 8.6063 Evaluate side-chains 55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128791 restraints weight = 5159.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131715 restraints weight = 3115.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133798 restraints weight = 2166.650| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2998 Z= 0.176 Angle : 0.664 8.736 4069 Z= 0.330 Chirality : 0.046 0.142 435 Planarity : 0.004 0.053 521 Dihedral : 5.645 50.526 436 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.57 % Allowed : 18.65 % Favored : 78.78 % 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: -1.92 (0.43), residues: 361 helix: -3.14 (1.25), residues: 13 sheet: -0.34 (0.51), residues: 120 loop : -1.76 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.031 0.002 PHE E 205 TYR 0.015 0.002 TYR E 225 ARG 0.002 0.000 ARG E 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 2.38756 ( 3) hydrogen bonds : bond 0.03774 ( 70) hydrogen bonds : angle 6.04224 ( 183) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.90907 ( 8) covalent geometry : bond 0.00423 ( 2993) covalent geometry : angle 0.66064 ( 4058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.307 Fit side-chains REVERT: E 83 ASN cc_start: 0.7887 (m110) cc_final: 0.7571 (m-40) outliers start: 8 outliers final: 8 residues processed: 53 average time/residue: 0.1139 time to fit residues: 7.9037 Evaluate side-chains 53 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 overall best weight: 0.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3808 r_free = 0.3808 target = 0.153898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134575 restraints weight = 5151.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137607 restraints weight = 3072.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139704 restraints weight = 2112.854| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2998 Z= 0.108 Angle : 0.613 9.285 4069 Z= 0.303 Chirality : 0.045 0.144 435 Planarity : 0.004 0.054 521 Dihedral : 5.395 55.265 436 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.57 % Allowed : 18.97 % Favored : 78.46 % 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 (0.44), residues: 361 helix: -2.88 (1.36), residues: 13 sheet: 0.02 (0.56), residues: 108 loop : -1.63 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.030 0.001 PHE C 486 TYR 0.018 0.001 TYR E 225 ARG 0.001 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 1) link_NAG-ASN : angle 1.50808 ( 3) hydrogen bonds : bond 0.03240 ( 70) hydrogen bonds : angle 5.90264 ( 183) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.58833 ( 8) covalent geometry : bond 0.00245 ( 2993) covalent geometry : angle 0.61197 ( 4058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.329 Fit side-chains REVERT: E 83 ASN cc_start: 0.7940 (m110) cc_final: 0.7700 (m-40) REVERT: E 205 PHE cc_start: 0.8538 (m-80) cc_final: 0.8242 (m-80) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.1132 time to fit residues: 8.1952 Evaluate side-chains 53 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.149905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130679 restraints weight = 5052.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133562 restraints weight = 3053.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135603 restraints weight = 2127.620| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2998 Z= 0.154 Angle : 0.629 8.302 4069 Z= 0.315 Chirality : 0.045 0.140 435 Planarity : 0.004 0.053 521 Dihedral : 5.478 50.947 436 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.93 % Allowed : 19.61 % Favored : 78.46 % 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: -1.71 (0.43), residues: 361 helix: -2.91 (1.45), residues: 13 sheet: 0.01 (0.55), residues: 107 loop : -1.67 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.027 0.002 PHE E 205 TYR 0.016 0.001 TYR E 225 ARG 0.002 0.000 ARG E 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 2.20349 ( 3) hydrogen bonds : bond 0.03546 ( 70) hydrogen bonds : angle 5.82712 ( 183) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.74673 ( 8) covalent geometry : bond 0.00379 ( 2993) covalent geometry : angle 0.62596 ( 4058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.59 seconds wall clock time: 27 minutes 29.01 seconds (1649.01 seconds total)