Starting phenix.real_space_refine on Wed Jun 4 15:21:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrz_32738/06_2025/7wrz_32738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrz_32738/06_2025/7wrz_32738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrz_32738/06_2025/7wrz_32738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrz_32738/06_2025/7wrz_32738.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrz_32738/06_2025/7wrz_32738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrz_32738/06_2025/7wrz_32738.cif" } resolution = 3.26 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= 0.001 sd= 0.055 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 2077 2.51 5 N 553 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.05, per 1000 atoms: 0.93 Number of scatterers: 3270 At special positions: 0 Unit cell: (84.24, 64.8, 71.28, 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 626 8.00 N 553 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 401.6 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 12.8% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.795A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.506A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.567A pdb=" N TYR R 369 " --> pdb=" O TYR R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 390 removed outlier: 3.550A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.622A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS H 96 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.539A pdb=" N ILE H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.596A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.343A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AA7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'R' and resid 473 through 474 103 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 834 1.46 - 1.57: 1460 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3355 Sorted by residual: bond pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" N ILE R 410 " pdb=" CA ILE R 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 3350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 4498 2.18 - 4.36: 56 4.36 - 6.55: 4 6.55 - 8.73: 0 8.73 - 10.91: 1 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta sigma weight residual 121.72 132.63 -10.91 1.54e+00 4.22e-01 5.02e+01 angle pdb=" C VAL R 382 " pdb=" N SER R 383 " pdb=" CA SER R 383 " ideal model delta sigma weight residual 120.49 114.45 6.04 1.42e+00 4.96e-01 1.81e+01 angle pdb=" N PHE R 374 " pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 110.79 114.90 -4.11 1.63e+00 3.76e-01 6.35e+00 angle pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " pdb=" CG PHE R 374 " ideal model delta sigma weight residual 113.80 116.26 -2.46 1.00e+00 1.00e+00 6.06e+00 angle pdb=" N TRP L 96 " pdb=" CA TRP L 96 " pdb=" C TRP L 96 " ideal model delta sigma weight residual 109.81 114.95 -5.14 2.21e+00 2.05e-01 5.42e+00 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1774 15.87 - 31.74: 168 31.74 - 47.61: 33 47.61 - 63.48: 9 63.48 - 79.34: 6 Dihedral angle restraints: 1990 sinusoidal: 794 harmonic: 1196 Sorted by residual: dihedral pdb=" CA TRP L 96 " pdb=" C TRP L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 134.00 46.00 0 5.00e+00 4.00e-02 8.47e+01 dihedral pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASP H 104 " pdb=" C ASP H 104 " pdb=" N TYR H 105 " pdb=" CA TYR H 105 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 ... (remaining 1987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 310 0.034 - 0.067: 124 0.067 - 0.101: 36 0.101 - 0.134: 21 0.134 - 0.168: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 96 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO L 97 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 41 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO L 42 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO L 46 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.018 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 243 2.74 - 3.28: 3077 3.28 - 3.82: 5219 3.82 - 4.36: 6717 4.36 - 4.90: 11797 Nonbonded interactions: 27053 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG L 56 " pdb=" O ILE L 60 " model vdw 2.301 3.120 nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR R 369 " pdb=" O PRO R 384 " model vdw 2.314 3.040 nonbonded pdb=" O ASP R 442 " pdb=" ND2 ASN R 448 " model vdw 2.367 3.120 ... (remaining 27048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.590 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.004 0.029 3363 Z= 0.169 Angle : 0.619 10.910 4577 Z= 0.355 Chirality : 0.044 0.168 492 Planarity : 0.005 0.066 587 Dihedral : 13.598 79.345 1212 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.03 (0.40), residues: 406 helix: -3.69 (0.60), residues: 27 sheet: -0.30 (0.41), residues: 152 loop : -0.47 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 436 HIS 0.002 0.001 HIS R 505 PHE 0.012 0.001 PHE R 347 TYR 0.015 0.001 TYR L 93 ARG 0.007 0.001 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 1.24696 ( 3) link_BETA1-4 : bond 0.00073 ( 1) link_BETA1-4 : angle 1.24355 ( 3) hydrogen bonds : bond 0.24946 ( 99) hydrogen bonds : angle 11.75452 ( 243) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.37689 ( 12) covalent geometry : bond 0.00362 ( 3355) covalent geometry : angle 0.61825 ( 4559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 GLU cc_start: 0.7411 (pm20) cc_final: 0.7185 (pm20) REVERT: L 84 ASP cc_start: 0.8096 (m-30) cc_final: 0.7859 (m-30) REVERT: R 340 GLU cc_start: 0.8306 (mp0) cc_final: 0.8014 (mm-30) REVERT: R 356 LYS cc_start: 0.9212 (mttp) cc_final: 0.8991 (mttm) REVERT: R 369 TYR cc_start: 0.7161 (m-80) cc_final: 0.6940 (m-80) REVERT: R 483 VAL cc_start: 0.7956 (t) cc_final: 0.7740 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2191 time to fit residues: 18.5168 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 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 = 0.3184 r_free = 0.3184 target = 0.108755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.091219 restraints weight = 4775.433| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.86 r_work: 0.3160 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3363 Z= 0.136 Angle : 0.541 5.724 4577 Z= 0.289 Chirality : 0.045 0.167 492 Planarity : 0.005 0.066 587 Dihedral : 5.338 44.081 502 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.15 % Allowed : 10.06 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.06 (0.40), residues: 406 helix: -3.39 (0.60), residues: 33 sheet: -0.36 (0.39), residues: 154 loop : -0.40 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.001 0.000 HIS H 35 PHE 0.012 0.001 PHE R 347 TYR 0.013 0.001 TYR L 93 ARG 0.005 0.001 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 1.12952 ( 3) link_BETA1-4 : bond 0.00207 ( 1) link_BETA1-4 : angle 1.20587 ( 3) hydrogen bonds : bond 0.04187 ( 99) hydrogen bonds : angle 7.67879 ( 243) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.58839 ( 12) covalent geometry : bond 0.00316 ( 3355) covalent geometry : angle 0.53979 ( 4559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.2159 time to fit residues: 15.9446 Evaluate side-chains 60 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 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 = 0.3144 r_free = 0.3144 target = 0.106186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.088847 restraints weight = 4613.911| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.83 r_work: 0.2784 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.004 0.027 3363 Z= 0.154 Angle : 0.528 5.777 4577 Z= 0.276 Chirality : 0.045 0.171 492 Planarity : 0.005 0.066 587 Dihedral : 5.319 44.333 502 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 1.72 % Allowed : 12.93 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.14 (0.40), residues: 406 helix: -3.56 (0.55), residues: 33 sheet: -0.46 (0.39), residues: 153 loop : -0.38 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.001 0.001 HIS R 505 PHE 0.011 0.001 PHE R 347 TYR 0.013 0.001 TYR L 93 ARG 0.004 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.09352 ( 3) link_BETA1-4 : bond 0.00041 ( 1) link_BETA1-4 : angle 1.35852 ( 3) hydrogen bonds : bond 0.03680 ( 99) hydrogen bonds : angle 7.03054 ( 243) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.55860 ( 12) covalent geometry : bond 0.00368 ( 3355) covalent geometry : angle 0.52601 ( 4559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8480 (mp10) cc_final: 0.7559 (mp10) REVERT: R 420 ASP cc_start: 0.9009 (m-30) cc_final: 0.8522 (m-30) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.2205 time to fit residues: 17.6502 Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.085657 restraints weight = 4766.236| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.87 r_work: 0.2743 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3363 Z= 0.227 Angle : 0.574 6.403 4577 Z= 0.299 Chirality : 0.047 0.186 492 Planarity : 0.005 0.067 587 Dihedral : 5.596 45.535 502 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.09 % Rotamer: Outliers : 2.30 % Allowed : 14.37 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.22 (0.40), residues: 406 helix: -3.75 (0.51), residues: 33 sheet: -0.48 (0.39), residues: 152 loop : -0.45 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 PHE 0.013 0.001 PHE R 347 TYR 0.015 0.002 TYR L 93 ARG 0.004 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.28086 ( 3) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 1.52478 ( 3) hydrogen bonds : bond 0.03613 ( 99) hydrogen bonds : angle 6.89464 ( 243) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.77776 ( 12) covalent geometry : bond 0.00541 ( 3355) covalent geometry : angle 0.57186 ( 4559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8572 (mp10) cc_final: 0.7667 (mp10) REVERT: R 369 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: R 420 ASP cc_start: 0.9004 (m-30) cc_final: 0.8378 (m-30) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.2402 time to fit residues: 17.8142 Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3095 r_free = 0.3095 target = 0.102699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.085383 restraints weight = 4700.112| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.86 r_work: 0.2734 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3363 Z= 0.214 Angle : 0.570 6.728 4577 Z= 0.295 Chirality : 0.046 0.181 492 Planarity : 0.005 0.067 587 Dihedral : 5.623 45.449 502 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 3.16 % Allowed : 15.52 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.19 (0.40), residues: 406 helix: -3.70 (0.55), residues: 33 sheet: -0.51 (0.40), residues: 152 loop : -0.39 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 PHE 0.011 0.001 PHE R 347 TYR 0.015 0.001 TYR L 93 ARG 0.006 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 1) link_NAG-ASN : angle 1.26451 ( 3) link_BETA1-4 : bond 0.00125 ( 1) link_BETA1-4 : angle 1.59246 ( 3) hydrogen bonds : bond 0.03545 ( 99) hydrogen bonds : angle 6.85038 ( 243) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.86880 ( 12) covalent geometry : bond 0.00511 ( 3355) covalent geometry : angle 0.56695 ( 4559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: R 357 ARG cc_start: 0.8567 (ttt90) cc_final: 0.8233 (ttt90) REVERT: R 369 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: R 394 ASN cc_start: 0.7867 (m-40) cc_final: 0.7471 (m110) REVERT: R 420 ASP cc_start: 0.9020 (m-30) cc_final: 0.8397 (m-30) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.2679 time to fit residues: 20.5185 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3121 r_free = 0.3121 target = 0.104339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.087040 restraints weight = 4883.256| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.88 r_work: 0.2761 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3363 Z= 0.146 Angle : 0.529 6.391 4577 Z= 0.275 Chirality : 0.045 0.158 492 Planarity : 0.005 0.066 587 Dihedral : 5.411 44.806 502 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.43 % Favored : 95.32 % Rotamer: Outliers : 3.45 % Allowed : 15.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.09 (0.41), residues: 406 helix: -4.07 (0.50), residues: 26 sheet: -0.37 (0.41), residues: 152 loop : -0.45 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE R 347 TYR 0.014 0.001 TYR L 93 ARG 0.005 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.06118 ( 3) link_BETA1-4 : bond 0.00151 ( 1) link_BETA1-4 : angle 1.56082 ( 3) hydrogen bonds : bond 0.03233 ( 99) hydrogen bonds : angle 6.73771 ( 243) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.80262 ( 12) covalent geometry : bond 0.00349 ( 3355) covalent geometry : angle 0.52665 ( 4559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8676 (mp10) cc_final: 0.7842 (mp10) REVERT: R 369 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6589 (m-80) REVERT: R 394 ASN cc_start: 0.7829 (m-40) cc_final: 0.7511 (m110) REVERT: R 420 ASP cc_start: 0.9038 (m-30) cc_final: 0.8445 (m-30) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.2237 time to fit residues: 18.9321 Evaluate side-chains 75 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3106 r_free = 0.3106 target = 0.103168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.085822 restraints weight = 4739.424| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.85 r_work: 0.2735 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3363 Z= 0.215 Angle : 0.566 6.824 4577 Z= 0.295 Chirality : 0.046 0.215 492 Planarity : 0.005 0.067 587 Dihedral : 5.578 45.410 502 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 3.45 % Allowed : 15.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.13 (0.41), residues: 406 helix: -4.09 (0.51), residues: 26 sheet: -0.37 (0.41), residues: 152 loop : -0.50 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 PHE 0.010 0.001 PHE R 374 TYR 0.015 0.001 TYR L 93 ARG 0.007 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 1.24025 ( 3) link_BETA1-4 : bond 0.00101 ( 1) link_BETA1-4 : angle 1.62042 ( 3) hydrogen bonds : bond 0.03380 ( 99) hydrogen bonds : angle 6.76885 ( 243) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.92836 ( 12) covalent geometry : bond 0.00521 ( 3355) covalent geometry : angle 0.56269 ( 4559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: L 84 ASP cc_start: 0.8560 (m-30) cc_final: 0.8263 (m-30) REVERT: R 369 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6539 (m-80) REVERT: R 394 ASN cc_start: 0.7844 (m-40) cc_final: 0.7605 (m110) REVERT: R 420 ASP cc_start: 0.9033 (m-30) cc_final: 0.8490 (m-30) REVERT: R 494 SER cc_start: 0.9176 (m) cc_final: 0.8885 (p) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.2212 time to fit residues: 16.8794 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 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 = 0.3112 r_free = 0.3112 target = 0.103654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.086450 restraints weight = 4666.728| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.84 r_work: 0.2756 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3363 Z= 0.182 Angle : 0.550 6.719 4577 Z= 0.287 Chirality : 0.046 0.199 492 Planarity : 0.005 0.067 587 Dihedral : 5.530 45.169 502 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 3.45 % Allowed : 16.09 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.12 (0.41), residues: 406 helix: -4.07 (0.51), residues: 26 sheet: -0.38 (0.41), residues: 152 loop : -0.49 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 PHE 0.008 0.001 PHE R 347 TYR 0.014 0.001 TYR L 93 ARG 0.007 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.19211 ( 3) link_BETA1-4 : bond 0.00140 ( 1) link_BETA1-4 : angle 1.63030 ( 3) hydrogen bonds : bond 0.03247 ( 99) hydrogen bonds : angle 6.72857 ( 243) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.90316 ( 12) covalent geometry : bond 0.00438 ( 3355) covalent geometry : angle 0.54621 ( 4559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: H 105 TYR cc_start: 0.9096 (m-80) cc_final: 0.8852 (m-80) REVERT: L 81 GLN cc_start: 0.8631 (mp10) cc_final: 0.7837 (mp10) REVERT: L 84 ASP cc_start: 0.8278 (m-30) cc_final: 0.8015 (m-30) REVERT: R 369 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: R 394 ASN cc_start: 0.7900 (m-40) cc_final: 0.7378 (m110) REVERT: R 420 ASP cc_start: 0.9027 (m-30) cc_final: 0.8484 (m-30) REVERT: R 494 SER cc_start: 0.9174 (m) cc_final: 0.8872 (p) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.2392 time to fit residues: 18.3918 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.086150 restraints weight = 4715.096| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.83 r_work: 0.2757 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3363 Z= 0.181 Angle : 0.548 6.763 4577 Z= 0.286 Chirality : 0.046 0.199 492 Planarity : 0.005 0.067 587 Dihedral : 5.539 45.212 502 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 3.16 % Allowed : 16.95 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.14 (0.41), residues: 406 helix: -4.06 (0.51), residues: 26 sheet: -0.41 (0.42), residues: 152 loop : -0.49 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 PHE 0.008 0.001 PHE R 347 TYR 0.015 0.001 TYR L 93 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 1.19333 ( 3) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 1.63745 ( 3) hydrogen bonds : bond 0.03243 ( 99) hydrogen bonds : angle 6.76965 ( 243) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.92836 ( 12) covalent geometry : bond 0.00435 ( 3355) covalent geometry : angle 0.54445 ( 4559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.332 Fit side-chains REVERT: L 81 GLN cc_start: 0.8552 (mp10) cc_final: 0.8000 (mt0) REVERT: L 84 ASP cc_start: 0.8643 (m-30) cc_final: 0.8169 (m-30) REVERT: R 369 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: R 420 ASP cc_start: 0.9039 (m-30) cc_final: 0.8528 (m-30) REVERT: R 494 SER cc_start: 0.9137 (m) cc_final: 0.8862 (p) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.2168 time to fit residues: 16.0764 Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.089007 restraints weight = 4596.937| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.73 r_work: 0.2864 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3363 Z= 0.124 Angle : 0.514 5.842 4577 Z= 0.270 Chirality : 0.045 0.179 492 Planarity : 0.005 0.066 587 Dihedral : 5.310 44.057 502 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.43 % Favored : 95.32 % Rotamer: Outliers : 3.45 % Allowed : 16.67 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.02 (0.41), residues: 406 helix: -3.96 (0.52), residues: 26 sheet: -0.32 (0.42), residues: 152 loop : -0.42 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 96 HIS 0.002 0.001 HIS H 35 PHE 0.006 0.001 PHE R 347 TYR 0.014 0.001 TYR L 93 ARG 0.007 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 0.98536 ( 3) link_BETA1-4 : bond 0.00179 ( 1) link_BETA1-4 : angle 1.58719 ( 3) hydrogen bonds : bond 0.02996 ( 99) hydrogen bonds : angle 6.59038 ( 243) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.76684 ( 12) covalent geometry : bond 0.00296 ( 3355) covalent geometry : angle 0.51097 ( 4559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.368 Fit side-chains REVERT: R 369 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: R 420 ASP cc_start: 0.8969 (m-30) cc_final: 0.8517 (m-30) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.1921 time to fit residues: 15.3380 Evaluate side-chains 64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN L 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.088736 restraints weight = 4656.849| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.74 r_work: 0.2779 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3363 Z= 0.149 Angle : 0.531 6.213 4577 Z= 0.278 Chirality : 0.045 0.187 492 Planarity : 0.005 0.066 587 Dihedral : 5.383 44.764 502 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 2.30 % Allowed : 19.25 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.03 (0.41), residues: 406 helix: -3.89 (0.53), residues: 26 sheet: -0.31 (0.42), residues: 152 loop : -0.45 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 PHE 0.007 0.001 PHE R 374 TYR 0.014 0.001 TYR L 93 ARG 0.007 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 1.02631 ( 3) link_BETA1-4 : bond 0.00139 ( 1) link_BETA1-4 : angle 1.61751 ( 3) hydrogen bonds : bond 0.03089 ( 99) hydrogen bonds : angle 6.53196 ( 243) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.79262 ( 12) covalent geometry : bond 0.00358 ( 3355) covalent geometry : angle 0.52829 ( 4559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.47 seconds wall clock time: 40 minutes 36.14 seconds (2436.14 seconds total)