Starting phenix.real_space_refine on Fri May 9 18:00:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vif_43260/05_2025/8vif_43260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vif_43260/05_2025/8vif_43260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vif_43260/05_2025/8vif_43260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vif_43260/05_2025/8vif_43260.map" model { file = "/net/cci-nas-00/data/ceres_data/8vif_43260/05_2025/8vif_43260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vif_43260/05_2025/8vif_43260.cif" } resolution = 3.1 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2109 2.51 5 N 557 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "R" 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: 3.34, per 1000 atoms: 1.00 Number of scatterers: 3326 At special positions: 0 Unit cell: (77.08, 81.78, 67.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 645 8.00 N 557 7.00 C 2109 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.04 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 NAG-ASN " NAG R1301 " - " ASN R 343 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 399.7 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 11.9% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.547A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 100A No H-bonds generated for 'chain 'H' and resid 99 through 100A' Processing helix chain 'L' and resid 27A through 30 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.598A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 372 removed outlier: 3.524A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.651A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.023A pdb=" N VAL H 35A" --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA H 96 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE H 100K" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.449A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 124 hydrogen bonds defined for protein. 279 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: 0.84 Time building geometry restraints manager: 0.86 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: 1060 1.34 - 1.46: 860 1.46 - 1.58: 1470 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3408 Sorted by residual: bond pdb=" C GLN H 39 " pdb=" N PRO H 40 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.15e-02 7.56e+03 6.15e+00 bond pdb=" N LYS H 43 " pdb=" CA LYS H 43 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.44e-02 4.82e+03 4.25e+00 bond pdb=" N GLY H 42 " pdb=" CA GLY H 42 " ideal model delta sigma weight residual 1.450 1.475 -0.025 1.38e-02 5.25e+03 3.22e+00 bond pdb=" C1 NAG R1301 " pdb=" O5 NAG R1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" CA LEU L 78 " pdb=" C LEU L 78 " ideal model delta sigma weight residual 1.529 1.517 0.012 1.04e-02 9.25e+03 1.31e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4311 1.07 - 2.14: 257 2.14 - 3.21: 49 3.21 - 4.28: 14 4.28 - 5.36: 4 Bond angle restraints: 4635 Sorted by residual: angle pdb=" N PRO H 40 " pdb=" CA PRO H 40 " pdb=" CB PRO H 40 " ideal model delta sigma weight residual 103.22 105.11 -1.89 5.20e-01 3.70e+00 1.32e+01 angle pdb=" C ASN L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 122.08 126.62 -4.54 1.47e+00 4.63e-01 9.52e+00 angle pdb=" CA GLY R 502 " pdb=" C GLY R 502 " pdb=" O GLY R 502 " ideal model delta sigma weight residual 122.29 120.15 2.14 8.10e-01 1.52e+00 6.96e+00 angle pdb=" CA LYS H 43 " pdb=" C LYS H 43 " pdb=" O LYS H 43 " ideal model delta sigma weight residual 121.49 118.46 3.03 1.16e+00 7.43e-01 6.80e+00 angle pdb=" CA GLY H 100C" pdb=" C GLY H 100C" pdb=" N TYR H 100D" ideal model delta sigma weight residual 114.85 117.19 -2.34 9.50e-01 1.11e+00 6.08e+00 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 1797 16.09 - 32.18: 173 32.18 - 48.26: 43 48.26 - 64.35: 12 64.35 - 80.44: 3 Dihedral angle restraints: 2028 sinusoidal: 794 harmonic: 1234 Sorted by residual: dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual 93.00 162.90 -69.90 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -45.89 -40.11 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA ASN H 97 " pdb=" C ASN H 97 " pdb=" N TYR H 98 " pdb=" CA TYR H 98 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 307 0.033 - 0.066: 139 0.066 - 0.100: 37 0.100 - 0.133: 25 0.133 - 0.166: 3 Chirality restraints: 511 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ASP H 99 " pdb=" N ASP H 99 " pdb=" C ASP H 99 " pdb=" CB ASP H 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 508 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 14 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO L 15 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO L 8 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 369 " 0.007 2.00e-02 2.50e+03 8.07e-03 1.30e+00 pdb=" CG TYR R 369 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR R 369 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR R 369 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 369 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 369 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 369 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 369 " 0.000 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 191 2.73 - 3.27: 3152 3.27 - 3.81: 5374 3.81 - 4.36: 6810 4.36 - 4.90: 11893 Nonbonded interactions: 27420 Sorted by model distance: nonbonded pdb=" O ASN H 31 " pdb=" OG SER H 53 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP H 55 " pdb=" NH1 ARG H 71 " model vdw 2.205 3.120 nonbonded pdb=" O ARG H 100F" pdb=" NH2 ARG L 96 " model vdw 2.364 3.120 nonbonded pdb=" NH2 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 2.368 3.120 nonbonded pdb=" OD1 ASN L 27B" pdb=" N ILE L 27C" model vdw 2.381 3.120 ... (remaining 27415 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.037 3415 Z= 0.174 Angle : 0.614 5.356 4650 Z= 0.359 Chirality : 0.045 0.166 511 Planarity : 0.006 0.095 596 Dihedral : 13.827 80.441 1224 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 14.40 % Favored : 85.60 % 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: 0.05 (0.40), residues: 419 helix: -2.67 (1.00), residues: 19 sheet: 0.80 (0.45), residues: 146 loop : -0.16 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.010 0.001 PHE L 91 TYR 0.020 0.002 TYR R 369 ARG 0.002 0.000 ARG R 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 0.72060 ( 3) hydrogen bonds : bond 0.19513 ( 112) hydrogen bonds : angle 8.91843 ( 279) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.69476 ( 12) covalent geometry : bond 0.00355 ( 3408) covalent geometry : angle 0.61321 ( 4635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.340 Fit side-chains REVERT: H 41 PRO cc_start: 0.8750 (Cg_endo) cc_final: 0.8532 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1653 time to fit residues: 9.9380 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3917 r_free = 0.3917 target = 0.169168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130935 restraints weight = 3475.151| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.68 r_work: 0.3123 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3415 Z= 0.144 Angle : 0.540 5.190 4650 Z= 0.289 Chirality : 0.045 0.151 511 Planarity : 0.005 0.065 596 Dihedral : 5.493 53.448 489 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.63 % Allowed : 14.67 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.40), residues: 419 helix: -2.97 (0.91), residues: 19 sheet: 0.57 (0.44), residues: 154 loop : 0.03 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.009 0.001 PHE L 62 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 1) link_NAG-ASN : angle 0.96267 ( 3) hydrogen bonds : bond 0.03505 ( 112) hydrogen bonds : angle 6.57409 ( 279) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.83569 ( 12) covalent geometry : bond 0.00331 ( 3408) covalent geometry : angle 0.53843 ( 4635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.333 Fit side-chains REVERT: H 43 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8264 (mttm) REVERT: H 56 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8013 (mm-30) REVERT: R 501 TYR cc_start: 0.7416 (m-10) cc_final: 0.7057 (m-10) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.1711 time to fit residues: 11.2455 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110124 restraints weight = 3530.241| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.26 r_work: 0.3105 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3415 Z= 0.154 Angle : 0.535 5.448 4650 Z= 0.284 Chirality : 0.045 0.152 511 Planarity : 0.005 0.052 596 Dihedral : 5.527 52.784 489 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.45 % Allowed : 16.03 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.40), residues: 419 helix: -3.03 (0.91), residues: 19 sheet: 0.40 (0.43), residues: 154 loop : -0.08 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.009 0.001 PHE L 91 TYR 0.020 0.002 TYR L 49 ARG 0.003 0.000 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 0.88290 ( 3) hydrogen bonds : bond 0.03122 ( 112) hydrogen bonds : angle 6.24074 ( 279) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.66618 ( 12) covalent geometry : bond 0.00357 ( 3408) covalent geometry : angle 0.53447 ( 4635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.355 Fit side-chains REVERT: H 43 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8373 (mttm) REVERT: R 501 TYR cc_start: 0.7547 (m-10) cc_final: 0.7241 (m-10) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.1323 time to fit residues: 9.0525 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128051 restraints weight = 3538.006| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.46 r_work: 0.3111 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3415 Z= 0.170 Angle : 0.544 6.007 4650 Z= 0.287 Chirality : 0.045 0.152 511 Planarity : 0.005 0.046 596 Dihedral : 5.580 52.915 489 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.99 % Allowed : 15.76 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.39), residues: 419 helix: -3.64 (0.73), residues: 25 sheet: 0.49 (0.44), residues: 144 loop : -0.15 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.009 0.001 PHE L 91 TYR 0.021 0.002 TYR L 49 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 0.90750 ( 3) hydrogen bonds : bond 0.02939 ( 112) hydrogen bonds : angle 6.21618 ( 279) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.66972 ( 12) covalent geometry : bond 0.00397 ( 3408) covalent geometry : angle 0.54307 ( 4635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.349 Fit side-chains REVERT: H 43 LYS cc_start: 0.8719 (mmtp) cc_final: 0.8392 (mttm) REVERT: H 108 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8757 (tt) REVERT: R 501 TYR cc_start: 0.7540 (m-10) cc_final: 0.7273 (m-10) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.1448 time to fit residues: 10.3208 Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3863 r_free = 0.3863 target = 0.164091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126430 restraints weight = 3556.044| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.49 r_work: 0.3022 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3415 Z= 0.185 Angle : 0.556 6.000 4650 Z= 0.295 Chirality : 0.046 0.155 511 Planarity : 0.005 0.042 596 Dihedral : 5.701 52.847 489 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.99 % Allowed : 16.03 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.39), residues: 419 helix: -3.74 (0.71), residues: 25 sheet: 0.39 (0.45), residues: 142 loop : -0.23 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.010 0.001 PHE L 91 TYR 0.022 0.002 TYR L 49 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 0.95112 ( 3) hydrogen bonds : bond 0.02974 ( 112) hydrogen bonds : angle 6.24628 ( 279) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.72277 ( 12) covalent geometry : bond 0.00434 ( 3408) covalent geometry : angle 0.55498 ( 4635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.326 Fit side-chains REVERT: H 43 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8366 (mttm) REVERT: H 108 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8740 (tt) REVERT: L 79 GLN cc_start: 0.7614 (mp10) cc_final: 0.6991 (mt0) REVERT: R 501 TYR cc_start: 0.7577 (m-10) cc_final: 0.7350 (m-10) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.1165 time to fit residues: 8.0484 Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.0040 chunk 33 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3720 r_free = 0.3720 target = 0.154706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108360 restraints weight = 3672.815| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.32 r_work: 0.2878 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3415 Z= 0.146 Angle : 0.526 5.408 4650 Z= 0.277 Chirality : 0.044 0.151 511 Planarity : 0.005 0.039 596 Dihedral : 5.579 53.015 489 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 16.03 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.39), residues: 419 helix: -3.72 (0.73), residues: 25 sheet: 0.41 (0.47), residues: 133 loop : -0.20 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 0.89318 ( 3) hydrogen bonds : bond 0.02717 ( 112) hydrogen bonds : angle 6.06189 ( 279) SS BOND : bond 0.00141 ( 6) SS BOND : angle 0.63154 ( 12) covalent geometry : bond 0.00339 ( 3408) covalent geometry : angle 0.52509 ( 4635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.338 Fit side-chains REVERT: H 108 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8701 (tt) REVERT: L 79 GLN cc_start: 0.7654 (mp10) cc_final: 0.6939 (mt0) REVERT: R 501 TYR cc_start: 0.7580 (m-10) cc_final: 0.7376 (m-10) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.1385 time to fit residues: 9.8244 Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108409 restraints weight = 3613.154| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.31 r_work: 0.2954 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3415 Z= 0.146 Angle : 0.517 5.383 4650 Z= 0.274 Chirality : 0.044 0.149 511 Planarity : 0.005 0.039 596 Dihedral : 5.549 52.912 489 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 17.93 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.39), residues: 419 helix: -3.70 (0.73), residues: 25 sheet: 0.44 (0.45), residues: 139 loop : -0.25 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.017 0.001 TYR L 49 ARG 0.005 0.000 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 0.91524 ( 3) hydrogen bonds : bond 0.02685 ( 112) hydrogen bonds : angle 6.00181 ( 279) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.63540 ( 12) covalent geometry : bond 0.00342 ( 3408) covalent geometry : angle 0.51677 ( 4635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.368 Fit side-chains REVERT: H 108 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8750 (tt) REVERT: L 79 GLN cc_start: 0.7651 (mp10) cc_final: 0.7030 (mt0) REVERT: R 386 LYS cc_start: 0.7704 (pttt) cc_final: 0.7340 (ptpp) REVERT: R 501 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7435 (m-10) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.1343 time to fit residues: 8.4720 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3641 r_free = 0.3641 target = 0.150615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103309 restraints weight = 3613.246| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.38 r_work: 0.3061 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3415 Z= 0.166 Angle : 0.554 7.238 4650 Z= 0.287 Chirality : 0.045 0.152 511 Planarity : 0.005 0.038 596 Dihedral : 5.615 52.901 489 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 18.48 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.39), residues: 419 helix: -3.05 (0.90), residues: 19 sheet: 0.37 (0.45), residues: 146 loop : -0.26 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 34 PHE 0.008 0.001 PHE L 91 TYR 0.019 0.001 TYR L 49 ARG 0.004 0.000 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 0.92725 ( 3) hydrogen bonds : bond 0.02768 ( 112) hydrogen bonds : angle 6.06372 ( 279) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.66391 ( 12) covalent geometry : bond 0.00391 ( 3408) covalent geometry : angle 0.55317 ( 4635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.362 Fit side-chains REVERT: H 86 ASP cc_start: 0.7844 (m-30) cc_final: 0.7643 (m-30) REVERT: L 79 GLN cc_start: 0.7634 (mp10) cc_final: 0.7080 (mt0) REVERT: R 386 LYS cc_start: 0.7733 (pttt) cc_final: 0.7412 (ptpp) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.1379 time to fit residues: 8.6821 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3840 r_free = 0.3840 target = 0.163334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129200 restraints weight = 3564.399| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.15 r_work: 0.3036 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3415 Z= 0.148 Angle : 0.526 6.223 4650 Z= 0.276 Chirality : 0.044 0.151 511 Planarity : 0.005 0.037 596 Dihedral : 5.576 52.955 489 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.63 % Allowed : 19.29 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.39), residues: 419 helix: -3.70 (0.74), residues: 25 sheet: 0.42 (0.45), residues: 139 loop : -0.24 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 0.91637 ( 3) hydrogen bonds : bond 0.02682 ( 112) hydrogen bonds : angle 6.00160 ( 279) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.61675 ( 12) covalent geometry : bond 0.00347 ( 3408) covalent geometry : angle 0.52589 ( 4635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7650 (mp10) cc_final: 0.7125 (mt0) REVERT: R 386 LYS cc_start: 0.7675 (pttt) cc_final: 0.7304 (ptpp) REVERT: R 501 TYR cc_start: 0.7598 (m-10) cc_final: 0.7262 (m-10) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.2085 time to fit residues: 12.8063 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3669 r_free = 0.3669 target = 0.151945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105401 restraints weight = 3581.081| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.32 r_work: 0.3079 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3415 Z= 0.157 Angle : 0.531 6.127 4650 Z= 0.279 Chirality : 0.045 0.151 511 Planarity : 0.005 0.037 596 Dihedral : 5.604 52.991 489 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.90 % Allowed : 19.02 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.39), residues: 419 helix: -2.96 (0.92), residues: 19 sheet: 0.22 (0.44), residues: 149 loop : -0.26 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.019 0.001 TYR L 49 ARG 0.004 0.001 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 0.89784 ( 3) hydrogen bonds : bond 0.02731 ( 112) hydrogen bonds : angle 6.02636 ( 279) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.64093 ( 12) covalent geometry : bond 0.00370 ( 3408) covalent geometry : angle 0.53023 ( 4635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.338 Fit side-chains REVERT: L 79 GLN cc_start: 0.7718 (mp10) cc_final: 0.7131 (mt0) REVERT: R 357 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7615 (ttp80) REVERT: R 386 LYS cc_start: 0.7636 (pttt) cc_final: 0.7260 (ptpp) REVERT: R 414 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8717 (mm-40) REVERT: R 501 TYR cc_start: 0.7529 (m-10) cc_final: 0.7158 (m-10) outliers start: 7 outliers final: 6 residues processed: 50 average time/residue: 0.1498 time to fit residues: 9.3863 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3654 r_free = 0.3654 target = 0.150778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103930 restraints weight = 3622.198| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.35 r_work: 0.3076 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3415 Z= 0.195 Angle : 0.557 6.173 4650 Z= 0.294 Chirality : 0.046 0.152 511 Planarity : 0.005 0.037 596 Dihedral : 5.775 53.080 489 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.90 % Allowed : 19.84 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.39), residues: 419 helix: -3.04 (0.90), residues: 19 sheet: 0.19 (0.44), residues: 146 loop : -0.27 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS L 34 PHE 0.009 0.001 PHE L 91 TYR 0.022 0.002 TYR L 49 ARG 0.004 0.001 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 0.89617 ( 3) hydrogen bonds : bond 0.02896 ( 112) hydrogen bonds : angle 6.17177 ( 279) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.68525 ( 12) covalent geometry : bond 0.00463 ( 3408) covalent geometry : angle 0.55665 ( 4635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.03 seconds wall clock time: 38 minutes 57.63 seconds (2337.63 seconds total)