Starting phenix.real_space_refine on Wed Sep 17 03:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vif_43260/09_2025/8vif_43260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vif_43260/09_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_43260/09_2025/8vif_43260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vif_43260/09_2025/8vif_43260.map" model { file = "/net/cci-nas-00/data/ceres_data/8vif_43260/09_2025/8vif_43260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vif_43260/09_2025/8vif_43260.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.19, per 1000 atoms: 0.36 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: 0.17 Conformation dependent library (CDL) restraints added in 133.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.42 Time building geometry restraints manager: 0.28 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG R 346 TYR 0.020 0.002 TYR R 369 PHE 0.010 0.001 PHE L 91 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3408) covalent geometry : angle 0.61321 ( 4635) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.69476 ( 12) hydrogen bonds : bond 0.19513 ( 112) hydrogen bonds : angle 8.91843 ( 279) link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 0.72060 ( 3) *********************** 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 : 0.124 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: 0.0694 time to fit residues: 4.1059 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.158162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110532 restraints weight = 3575.366| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.37 r_work: 0.2973 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3415 Z= 0.208 Angle : 0.592 5.938 4650 Z= 0.316 Chirality : 0.047 0.156 511 Planarity : 0.006 0.064 596 Dihedral : 5.723 53.443 489 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.90 % Allowed : 15.76 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.40), residues: 419 helix: -3.15 (0.89), residues: 19 sheet: 0.45 (0.44), residues: 152 loop : -0.06 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 403 TYR 0.024 0.002 TYR L 49 PHE 0.013 0.001 PHE L 91 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 3408) covalent geometry : angle 0.59024 ( 4635) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.93096 ( 12) hydrogen bonds : bond 0.03844 ( 112) hydrogen bonds : angle 6.74229 ( 279) link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 0.99361 ( 3) *********************** 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 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.082 Fit side-chains REVERT: H 43 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8331 (mttm) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.0773 time to fit residues: 4.8520 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 : 0.131 ------------------------------------------------------------------------------- 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 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 12 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.155357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107959 restraints weight = 3537.104| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.34 r_work: 0.2989 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3415 Z= 0.186 Angle : 0.564 5.740 4650 Z= 0.300 Chirality : 0.046 0.154 511 Planarity : 0.005 0.052 596 Dihedral : 5.707 52.779 489 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.72 % Allowed : 15.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.39), residues: 419 helix: -3.80 (0.70), residues: 25 sheet: 0.43 (0.44), residues: 144 loop : -0.15 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 18 TYR 0.022 0.002 TYR L 49 PHE 0.011 0.001 PHE L 91 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3408) covalent geometry : angle 0.56333 ( 4635) SS BOND : bond 0.00337 ( 6) SS BOND : angle 0.76723 ( 12) hydrogen bonds : bond 0.03383 ( 112) hydrogen bonds : angle 6.43059 ( 279) link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 0.88500 ( 3) *********************** 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 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.131 Fit side-chains REVERT: H 43 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8385 (mttm) REVERT: R 501 TYR cc_start: 0.7549 (m-10) cc_final: 0.7214 (m-10) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0694 time to fit residues: 4.6812 Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 14 optimal weight: 0.0070 chunk 17 optimal weight: 0.0000 chunk 25 optimal weight: 0.0470 overall best weight: 0.1516 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.162646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117116 restraints weight = 3573.231| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.30 r_work: 0.3050 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3415 Z= 0.093 Angle : 0.485 4.561 4650 Z= 0.256 Chirality : 0.043 0.142 511 Planarity : 0.005 0.047 596 Dihedral : 5.293 53.129 489 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.90 % Allowed : 16.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.40), residues: 419 helix: -3.81 (0.67), residues: 27 sheet: 0.49 (0.44), residues: 147 loop : 0.06 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.010 0.001 TYR L 49 PHE 0.007 0.001 PHE L 91 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3408) covalent geometry : angle 0.48435 ( 4635) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.52735 ( 12) hydrogen bonds : bond 0.02512 ( 112) hydrogen bonds : angle 5.91284 ( 279) link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 0.82486 ( 3) *********************** 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 62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.147 Fit side-chains REVERT: H 18 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7463 (tt) REVERT: L 18 ARG cc_start: 0.8128 (ttt-90) cc_final: 0.7817 (ttt180) REVERT: L 32 ASP cc_start: 0.8352 (m-30) cc_final: 0.8143 (m-30) REVERT: R 501 TYR cc_start: 0.7410 (m-10) cc_final: 0.7193 (m-10) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0716 time to fit residues: 5.0425 Evaluate side-chains 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN R 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106212 restraints weight = 3629.701| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.30 r_work: 0.2927 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1670 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= 0.209 Angle : 0.566 6.970 4650 Z= 0.298 Chirality : 0.046 0.150 511 Planarity : 0.005 0.045 596 Dihedral : 5.680 52.783 489 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.72 % Allowed : 17.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.39), residues: 419 helix: -3.88 (0.68), residues: 25 sheet: 0.43 (0.44), residues: 144 loop : -0.16 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 403 TYR 0.025 0.002 TYR L 49 PHE 0.009 0.001 PHE L 91 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3408) covalent geometry : angle 0.56545 ( 4635) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.75035 ( 12) hydrogen bonds : bond 0.03101 ( 112) hydrogen bonds : angle 6.24515 ( 279) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 0.94833 ( 3) *********************** 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: 10 poor density : 47 time to evaluate : 0.132 Fit side-chains REVERT: H 18 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7858 (tp) REVERT: L 79 GLN cc_start: 0.7588 (mp10) cc_final: 0.6864 (mt0) REVERT: R 501 TYR cc_start: 0.7552 (m-10) cc_final: 0.7291 (m-10) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.0514 time to fit residues: 3.4358 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 : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 6 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.155804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109721 restraints weight = 3604.236| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.32 r_work: 0.2910 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1773 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= 0.156 Angle : 0.523 6.344 4650 Z= 0.276 Chirality : 0.045 0.149 511 Planarity : 0.005 0.041 596 Dihedral : 5.588 53.038 489 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 17.39 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.40), residues: 419 helix: -3.94 (0.68), residues: 25 sheet: 0.27 (0.44), residues: 147 loop : -0.08 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 403 TYR 0.019 0.001 TYR L 49 PHE 0.008 0.001 PHE L 91 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.000 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3408) covalent geometry : angle 0.52278 ( 4635) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.58645 ( 12) hydrogen bonds : bond 0.02759 ( 112) hydrogen bonds : angle 6.03319 ( 279) link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 0.89048 ( 3) *********************** 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 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.144 Fit side-chains REVERT: H 18 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7862 (tp) REVERT: L 79 GLN cc_start: 0.7708 (mp10) cc_final: 0.6954 (mt0) REVERT: R 501 TYR cc_start: 0.7486 (m-10) cc_final: 0.7235 (m-10) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.0510 time to fit residues: 3.2525 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 ASP 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 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 34 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.152669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.105349 restraints weight = 3712.581| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.38 r_work: 0.2901 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1903 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= 0.162 Angle : 0.525 6.709 4650 Z= 0.277 Chirality : 0.045 0.148 511 Planarity : 0.005 0.040 596 Dihedral : 5.578 52.912 489 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 17.93 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.40), residues: 419 helix: -3.99 (0.67), residues: 25 sheet: 0.32 (0.44), residues: 144 loop : -0.09 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 403 TYR 0.019 0.001 TYR L 49 PHE 0.008 0.001 PHE L 91 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.000 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3408) covalent geometry : angle 0.52447 ( 4635) SS BOND : bond 0.00201 ( 6) SS BOND : angle 0.64005 ( 12) hydrogen bonds : bond 0.02774 ( 112) hydrogen bonds : angle 6.00979 ( 279) link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 0.92621 ( 3) *********************** 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: 8 poor density : 45 time to evaluate : 0.089 Fit side-chains REVERT: L 79 GLN cc_start: 0.7610 (mp10) cc_final: 0.7015 (mt0) REVERT: R 386 LYS cc_start: 0.7715 (pttt) cc_final: 0.7308 (ptpp) REVERT: R 501 TYR cc_start: 0.7620 (m-10) cc_final: 0.7413 (m-10) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.0507 time to fit residues: 3.2617 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER 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 441 LEU Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.151611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105185 restraints weight = 3747.673| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.33 r_work: 0.2880 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3415 Z= 0.216 Angle : 0.568 7.268 4650 Z= 0.298 Chirality : 0.046 0.152 511 Planarity : 0.005 0.038 596 Dihedral : 5.774 52.841 489 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.99 % Allowed : 17.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.39), residues: 419 helix: -4.10 (0.63), residues: 25 sheet: 0.22 (0.44), residues: 142 loop : -0.17 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 403 TYR 0.024 0.002 TYR L 49 PHE 0.009 0.001 PHE L 91 TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3408) covalent geometry : angle 0.56690 ( 4635) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.73953 ( 12) hydrogen bonds : bond 0.03037 ( 112) hydrogen bonds : angle 6.20938 ( 279) link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 0.95171 ( 3) *********************** 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 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.178 Fit side-chains REVERT: L 79 GLN cc_start: 0.7730 (mp10) cc_final: 0.7029 (mt0) REVERT: R 386 LYS cc_start: 0.7703 (pttt) cc_final: 0.7274 (ptpp) REVERT: R 501 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7351 (m-10) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.0624 time to fit residues: 4.2269 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER 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 501 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.151703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105539 restraints weight = 3636.134| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.33 r_work: 0.3031 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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= 0.147 Angle : 0.520 6.477 4650 Z= 0.273 Chirality : 0.044 0.150 511 Planarity : 0.005 0.038 596 Dihedral : 5.580 52.994 489 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.40), residues: 419 helix: -4.03 (0.66), residues: 25 sheet: 0.26 (0.45), residues: 142 loop : -0.10 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 403 TYR 0.017 0.001 TYR L 49 PHE 0.007 0.001 PHE L 91 TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3408) covalent geometry : angle 0.51921 ( 4635) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.62227 ( 12) hydrogen bonds : bond 0.02690 ( 112) hydrogen bonds : angle 5.96090 ( 279) link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 0.91135 ( 3) *********************** 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 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.100 Fit side-chains REVERT: L 79 GLN cc_start: 0.7752 (mp10) cc_final: 0.7137 (mt0) REVERT: R 386 LYS cc_start: 0.7646 (pttt) cc_final: 0.7251 (ptpp) REVERT: R 414 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8746 (mm-40) REVERT: R 501 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7393 (m-10) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.0577 time to fit residues: 3.5834 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER 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 Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 9 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 = 0.3648 r_free = 0.3648 target = 0.150526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104220 restraints weight = 3633.726| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.34 r_work: 0.2931 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2124 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= 0.183 Angle : 0.535 7.006 4650 Z= 0.284 Chirality : 0.045 0.150 511 Planarity : 0.005 0.038 596 Dihedral : 5.669 52.902 489 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.99 % Allowed : 17.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.40), residues: 419 helix: -4.11 (0.64), residues: 25 sheet: 0.24 (0.45), residues: 142 loop : -0.11 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 403 TYR 0.021 0.002 TYR L 49 PHE 0.009 0.001 PHE L 91 TRP 0.013 0.002 TRP H 47 HIS 0.001 0.000 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 3408) covalent geometry : angle 0.53467 ( 4635) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.67337 ( 12) hydrogen bonds : bond 0.02873 ( 112) hydrogen bonds : angle 6.07743 ( 279) link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 0.94671 ( 3) ********************** 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 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.132 Fit side-chains REVERT: H 82 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7981 (mtp) REVERT: L 79 GLN cc_start: 0.7671 (mp10) cc_final: 0.7050 (mt0) REVERT: R 386 LYS cc_start: 0.7624 (pttt) cc_final: 0.7238 (ptpp) REVERT: R 414 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8750 (mm-40) REVERT: R 501 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.7395 (m-10) outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.0528 time to fit residues: 3.6993 Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET 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 470 THR Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 37 optimal weight: 0.0270 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.154455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108344 restraints weight = 3664.270| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.36 r_work: 0.3069 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3415 Z= 0.101 Angle : 0.480 5.701 4650 Z= 0.254 Chirality : 0.043 0.144 511 Planarity : 0.004 0.037 596 Dihedral : 5.334 53.120 489 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.63 % Allowed : 19.57 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.40), residues: 419 helix: -4.07 (0.66), residues: 27 sheet: 0.42 (0.45), residues: 139 loop : 0.03 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.012 0.001 TYR L 49 PHE 0.006 0.001 PHE L 91 TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3408) covalent geometry : angle 0.47905 ( 4635) SS BOND : bond 0.00151 ( 6) SS BOND : angle 0.51360 ( 12) hydrogen bonds : bond 0.02381 ( 112) hydrogen bonds : angle 5.68073 ( 279) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 0.89128 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.30 seconds wall clock time: 21 minutes 16.79 seconds (1276.79 seconds total)