Starting phenix.real_space_refine on Tue Mar 3 13:17:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7b_23709/03_2026/7m7b_23709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7b_23709/03_2026/7m7b_23709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2026/7m7b_23709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2026/7m7b_23709.map" model { file = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2026/7m7b_23709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2026/7m7b_23709.cif" } resolution = 2.95 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= 0.056 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 17 5.16 5 C 3103 2.51 5 N 820 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain: "L" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1591 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.24, per 1000 atoms: 0.25 Number of scatterers: 4898 At special positions: 0 Unit cell: (105.692, 91.4418, 104.505, 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 17 16.00 O 958 8.00 N 820 7.00 C 3103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.02 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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 A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 261.1 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 12.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.758A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.833A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.674A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.764A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.594A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.753A pdb=" N ILE H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.541A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 149 through 152 203 hydrogen bonds defined for protein. 486 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: 0.82 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1318 1.33 - 1.46: 990 1.46 - 1.58: 2703 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 5029 Sorted by residual: bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" CZ ARG H 98 " pdb=" NH2 ARG H 98 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 5024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4771 1.87 - 3.74: 1779 3.74 - 5.61: 278 5.61 - 7.49: 34 7.49 - 9.36: 1 Bond angle restraints: 6863 Sorted by residual: angle pdb=" CA ASP H 106 " pdb=" CB ASP H 106 " pdb=" CG ASP H 106 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA VAL L 163 " pdb=" CB VAL L 163 " pdb=" CG1 VAL L 163 " ideal model delta sigma weight residual 110.40 119.76 -9.36 1.70e+00 3.46e-01 3.03e+01 angle pdb=" N LYS H 143 " pdb=" CA LYS H 143 " pdb=" C LYS H 143 " ideal model delta sigma weight residual 111.69 118.38 -6.69 1.23e+00 6.61e-01 2.96e+01 angle pdb=" CA PHE H 78 " pdb=" CB PHE H 78 " pdb=" CG PHE H 78 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 angle pdb=" CB HIS H 53 " pdb=" CG HIS H 53 " pdb=" CD2 HIS H 53 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 ... (remaining 6858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2762 17.30 - 34.60: 204 34.60 - 51.90: 28 51.90 - 69.21: 11 69.21 - 86.51: 4 Dihedral angle restraints: 3009 sinusoidal: 1171 harmonic: 1838 Sorted by residual: dihedral pdb=" CA VAL H 142 " pdb=" C VAL H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO H 185 " pdb=" C PRO H 185 " pdb=" N SER H 186 " pdb=" CA SER H 186 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA VAL L 109 " pdb=" C VAL L 109 " pdb=" N LEU L 110 " pdb=" CA LEU L 110 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 3006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 534 0.104 - 0.207: 191 0.207 - 0.311: 29 0.311 - 0.414: 8 0.414 - 0.518: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA ASN L 173 " pdb=" N ASN L 173 " pdb=" C ASN L 173 " pdb=" CB ASN L 173 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA SER H 15 " pdb=" N SER H 15 " pdb=" C SER H 15 " pdb=" CB SER H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 761 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 152 " 0.143 2.00e-02 2.50e+03 7.99e-02 1.60e+02 pdb=" CG TRP L 152 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP L 152 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 152 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP L 152 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP L 152 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP L 152 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 152 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 152 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP L 152 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " 0.131 2.00e-02 2.50e+03 7.23e-02 1.05e+02 pdb=" CG TYR A 495 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " -0.114 2.00e-02 2.50e+03 6.29e-02 7.91e+01 pdb=" CG TYR L 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " -0.096 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2340 2.99 - 3.47: 4488 3.47 - 3.94: 8045 3.94 - 4.42: 8899 4.42 - 4.90: 15303 Nonbonded interactions: 39075 Sorted by model distance: nonbonded pdb=" N GLU L 51 " pdb=" O GLU L 51 " model vdw 2.512 2.496 nonbonded pdb=" OD2 ASP L 68 " pdb=" OG SER L 71 " model vdw 2.559 3.040 nonbonded pdb=" OD1 ASP L 68 " pdb=" OG SER L 70 " model vdw 2.562 3.040 nonbonded pdb=" OH TYR H 145 " pdb=" OE2 GLU H 148 " model vdw 2.568 3.040 nonbonded pdb=" OE2 GLU L 128 " pdb=" OG1 THR L 135 " model vdw 2.568 3.040 ... (remaining 39070 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: 3.720 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.240 Find NCS groups from input model: 0.040 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:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.012 0.065 5039 Z= 0.741 Angle : 1.877 9.357 6885 Z= 1.251 Chirality : 0.108 0.518 764 Planarity : 0.015 0.172 881 Dihedral : 13.017 86.508 1813 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: -0.73 (0.32), residues: 629 helix: -3.61 (0.50), residues: 41 sheet: 0.44 (0.37), residues: 200 loop : -0.61 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 55 TYR 0.131 0.021 TYR A 495 PHE 0.074 0.014 PHE H 29 TRP 0.143 0.019 TRP L 152 HIS 0.011 0.004 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.01241 ( 5029) covalent geometry : angle 1.87442 ( 6863) SS BOND : bond 0.01119 ( 8) SS BOND : angle 1.53725 ( 16) hydrogen bonds : bond 0.14397 ( 181) hydrogen bonds : angle 8.85591 ( 486) link_NAG-ASN : bond 0.01155 ( 2) link_NAG-ASN : angle 4.42540 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7689 (p0) cc_final: 0.7397 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.7389 time to fit residues: 29.1222 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 437 ASN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039348 restraints weight = 21858.034| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.45 r_work: 0.2750 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 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 : 0.003 0.027 5039 Z= 0.137 Angle : 0.621 5.261 6885 Z= 0.341 Chirality : 0.047 0.186 764 Planarity : 0.005 0.041 881 Dihedral : 6.142 23.980 727 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.55 % Allowed : 5.69 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: -0.25 (0.32), residues: 629 helix: -2.69 (0.70), residues: 41 sheet: 0.53 (0.34), residues: 218 loop : -0.23 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.027 0.001 TYR A 369 PHE 0.018 0.001 PHE H 78 TRP 0.013 0.001 TRP L 152 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5029) covalent geometry : angle 0.61949 ( 6863) SS BOND : bond 0.00307 ( 8) SS BOND : angle 0.52504 ( 16) hydrogen bonds : bond 0.03728 ( 181) hydrogen bonds : angle 6.31482 ( 486) link_NAG-ASN : bond 0.00189 ( 2) link_NAG-ASN : angle 1.81061 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8847 (tp30) REVERT: A 428 ASP cc_start: 0.9388 (p0) cc_final: 0.9125 (p0) REVERT: L 84 GLU cc_start: 0.9050 (pm20) cc_final: 0.8609 (pm20) REVERT: L 85 ASP cc_start: 0.8054 (m-30) cc_final: 0.7755 (m-30) REVERT: L 164 GLU cc_start: 0.7496 (pt0) cc_final: 0.7196 (pm20) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.7403 time to fit residues: 22.2747 Evaluate side-chains 22 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.052751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.037814 restraints weight = 21824.590| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.38 r_work: 0.2705 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5039 Z= 0.276 Angle : 0.650 5.228 6885 Z= 0.354 Chirality : 0.048 0.194 764 Planarity : 0.005 0.043 881 Dihedral : 6.073 22.730 727 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.55 % Allowed : 7.71 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: -0.28 (0.33), residues: 629 helix: -2.51 (0.76), residues: 35 sheet: 0.61 (0.35), residues: 224 loop : -0.41 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 346 TYR 0.024 0.002 TYR A 369 PHE 0.014 0.002 PHE H 78 TRP 0.011 0.002 TRP H 47 HIS 0.004 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 5029) covalent geometry : angle 0.64751 ( 6863) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.82364 ( 16) hydrogen bonds : bond 0.04063 ( 181) hydrogen bonds : angle 6.32652 ( 486) link_NAG-ASN : bond 0.00231 ( 2) link_NAG-ASN : angle 1.79285 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8831 (tp30) REVERT: A 428 ASP cc_start: 0.9396 (p0) cc_final: 0.9145 (p0) REVERT: H 5 GLN cc_start: 0.9119 (tp40) cc_final: 0.8911 (tp40) REVERT: L 84 GLU cc_start: 0.9024 (pm20) cc_final: 0.8770 (pm20) REVERT: L 85 ASP cc_start: 0.8127 (m-30) cc_final: 0.7835 (m-30) REVERT: L 164 GLU cc_start: 0.7571 (pt0) cc_final: 0.7319 (pm20) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.6930 time to fit residues: 20.2469 Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.053190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038505 restraints weight = 21685.907| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.32 r_work: 0.2733 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5039 Z= 0.146 Angle : 0.568 7.982 6885 Z= 0.304 Chirality : 0.046 0.176 764 Planarity : 0.005 0.043 881 Dihedral : 5.399 22.283 727 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.92 % Allowed : 8.62 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: -0.14 (0.33), residues: 629 helix: -2.41 (0.74), residues: 35 sheet: 0.66 (0.35), residues: 224 loop : -0.28 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.022 0.001 TYR A 369 PHE 0.012 0.001 PHE H 78 TRP 0.009 0.001 TRP L 189 HIS 0.003 0.001 HIS L 201 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5029) covalent geometry : angle 0.56613 ( 6863) SS BOND : bond 0.00266 ( 8) SS BOND : angle 0.57566 ( 16) hydrogen bonds : bond 0.03480 ( 181) hydrogen bonds : angle 5.95578 ( 486) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.61136 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9356 (p0) cc_final: 0.9061 (p0) REVERT: L 84 GLU cc_start: 0.8990 (pm20) cc_final: 0.8773 (pm20) REVERT: L 85 ASP cc_start: 0.8105 (m-30) cc_final: 0.7598 (m-30) outliers start: 5 outliers final: 1 residues processed: 26 average time/residue: 0.6420 time to fit residues: 17.4040 Evaluate side-chains 19 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037683 restraints weight = 22036.936| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.25 r_work: 0.2702 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5039 Z= 0.233 Angle : 0.614 8.326 6885 Z= 0.329 Chirality : 0.047 0.181 764 Planarity : 0.005 0.043 881 Dihedral : 5.546 21.644 727 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.37 % Allowed : 10.83 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: -0.26 (0.33), residues: 629 helix: -2.74 (0.63), residues: 41 sheet: 0.66 (0.35), residues: 224 loop : -0.35 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 346 TYR 0.022 0.001 TYR A 369 PHE 0.013 0.001 PHE H 78 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 5029) covalent geometry : angle 0.61263 ( 6863) SS BOND : bond 0.00270 ( 8) SS BOND : angle 0.68821 ( 16) hydrogen bonds : bond 0.03787 ( 181) hydrogen bonds : angle 6.07742 ( 486) link_NAG-ASN : bond 0.00222 ( 2) link_NAG-ASN : angle 1.62312 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9332 (p0) cc_final: 0.9028 (p0) REVERT: A 537 LYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5700 (pptt) REVERT: L 84 GLU cc_start: 0.9028 (pm20) cc_final: 0.8801 (pm20) REVERT: L 164 GLU cc_start: 0.7356 (pt0) cc_final: 0.7140 (pm20) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.6458 time to fit residues: 15.5935 Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.053362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038684 restraints weight = 22215.132| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.33 r_work: 0.2736 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5039 Z= 0.125 Angle : 0.554 10.109 6885 Z= 0.294 Chirality : 0.045 0.169 764 Planarity : 0.005 0.043 881 Dihedral : 4.987 20.964 727 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.55 % Allowed : 12.48 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: -0.09 (0.33), residues: 629 helix: -2.50 (0.66), residues: 40 sheet: 0.71 (0.35), residues: 224 loop : -0.21 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.021 0.001 TYR A 369 PHE 0.011 0.001 PHE H 78 TRP 0.010 0.001 TRP H 100 HIS 0.001 0.000 HIS L 201 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5029) covalent geometry : angle 0.55288 ( 6863) SS BOND : bond 0.00234 ( 8) SS BOND : angle 0.48766 ( 16) hydrogen bonds : bond 0.03302 ( 181) hydrogen bonds : angle 5.74322 ( 486) link_NAG-ASN : bond 0.00043 ( 2) link_NAG-ASN : angle 1.53696 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8646 (mp0) REVERT: A 428 ASP cc_start: 0.9353 (p0) cc_final: 0.9046 (p0) REVERT: H 3 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (tm-30) REVERT: L 85 ASP cc_start: 0.8141 (m-30) cc_final: 0.7678 (m-30) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.8018 time to fit residues: 20.8343 Evaluate side-chains 19 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.2980 chunk 13 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.054154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039302 restraints weight = 21618.718| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.33 r_work: 0.2765 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5039 Z= 0.101 Angle : 0.544 10.280 6885 Z= 0.288 Chirality : 0.045 0.167 764 Planarity : 0.005 0.041 881 Dihedral : 4.700 20.171 727 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.73 % Allowed : 13.03 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: 0.07 (0.34), residues: 629 helix: -2.38 (0.74), residues: 34 sheet: 0.84 (0.36), residues: 224 loop : -0.15 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.021 0.001 TYR A 369 PHE 0.010 0.001 PHE H 78 TRP 0.011 0.001 TRP H 100 HIS 0.001 0.000 HIS L 201 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5029) covalent geometry : angle 0.54308 ( 6863) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.44612 ( 16) hydrogen bonds : bond 0.03199 ( 181) hydrogen bonds : angle 5.54215 ( 486) link_NAG-ASN : bond 0.00105 ( 2) link_NAG-ASN : angle 1.45066 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.235 Fit side-chains REVERT: A 340 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8655 (mp0) REVERT: A 428 ASP cc_start: 0.9324 (p0) cc_final: 0.9015 (p0) REVERT: H 3 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8350 (tm130) REVERT: H 5 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8700 (mm-40) REVERT: L 86 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8039 (mt-10) REVERT: L 164 GLU cc_start: 0.7378 (pm20) cc_final: 0.6759 (pt0) outliers start: 4 outliers final: 0 residues processed: 24 average time/residue: 0.6758 time to fit residues: 16.9677 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 171 GLN L 1 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.053618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038856 restraints weight = 22234.724| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.29 r_work: 0.2745 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5039 Z= 0.124 Angle : 0.556 12.165 6885 Z= 0.287 Chirality : 0.044 0.166 764 Planarity : 0.005 0.040 881 Dihedral : 4.686 20.589 727 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.55 % Allowed : 13.76 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: 0.10 (0.34), residues: 629 helix: -2.24 (0.79), residues: 34 sheet: 0.84 (0.36), residues: 224 loop : -0.14 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 210 TYR 0.021 0.001 TYR A 369 PHE 0.011 0.001 PHE H 78 TRP 0.023 0.001 TRP L 189 HIS 0.001 0.000 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5029) covalent geometry : angle 0.55497 ( 6863) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.49630 ( 16) hydrogen bonds : bond 0.03193 ( 181) hydrogen bonds : angle 5.55554 ( 486) link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 1.41214 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.153 Fit side-chains REVERT: A 340 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8681 (mp0) REVERT: A 428 ASP cc_start: 0.9324 (p0) cc_final: 0.9001 (p0) REVERT: H 3 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: L 86 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8062 (mt-10) outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 0.7639 time to fit residues: 18.3210 Evaluate side-chains 22 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.039356 restraints weight = 21583.746| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.25 r_work: 0.2768 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5039 Z= 0.107 Angle : 0.557 11.740 6885 Z= 0.288 Chirality : 0.044 0.163 764 Planarity : 0.004 0.038 881 Dihedral : 4.539 20.366 727 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.92 % Allowed : 13.94 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: 0.16 (0.34), residues: 629 helix: -2.07 (0.82), residues: 34 sheet: 0.86 (0.36), residues: 223 loop : -0.09 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.020 0.001 TYR A 369 PHE 0.010 0.001 PHE H 78 TRP 0.020 0.001 TRP L 189 HIS 0.001 0.000 HIS L 201 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5029) covalent geometry : angle 0.55630 ( 6863) SS BOND : bond 0.00200 ( 8) SS BOND : angle 0.44581 ( 16) hydrogen bonds : bond 0.03071 ( 181) hydrogen bonds : angle 5.43249 ( 486) link_NAG-ASN : bond 0.00090 ( 2) link_NAG-ASN : angle 1.39400 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.200 Fit side-chains REVERT: A 340 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8653 (mp0) REVERT: A 428 ASP cc_start: 0.9310 (p0) cc_final: 0.8984 (p0) REVERT: H 3 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: L 86 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8027 (mt-10) REVERT: L 164 GLU cc_start: 0.7227 (pm20) cc_final: 0.6310 (pt0) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.6564 time to fit residues: 17.1970 Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 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 3 GLN H 5 GLN L 1 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.039148 restraints weight = 21620.198| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.30 r_work: 0.2761 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5039 Z= 0.113 Angle : 0.556 12.380 6885 Z= 0.287 Chirality : 0.044 0.164 764 Planarity : 0.004 0.037 881 Dihedral : 4.519 20.370 727 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.73 % Allowed : 14.13 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: 0.17 (0.34), residues: 629 helix: -2.05 (0.82), residues: 34 sheet: 0.87 (0.36), residues: 224 loop : -0.09 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 210 TYR 0.021 0.001 TYR A 369 PHE 0.011 0.001 PHE H 78 TRP 0.018 0.001 TRP L 189 HIS 0.001 0.000 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5029) covalent geometry : angle 0.55535 ( 6863) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.46471 ( 16) hydrogen bonds : bond 0.03122 ( 181) hydrogen bonds : angle 5.41458 ( 486) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.37548 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.186 Fit side-chains REVERT: A 340 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8652 (mp0) REVERT: A 428 ASP cc_start: 0.9309 (p0) cc_final: 0.8973 (p0) REVERT: L 86 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8047 (mt-10) REVERT: L 164 GLU cc_start: 0.7282 (pm20) cc_final: 0.6370 (pt0) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.6466 time to fit residues: 14.9157 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.038916 restraints weight = 21805.297| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.29 r_work: 0.2753 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5039 Z= 0.126 Angle : 0.556 10.182 6885 Z= 0.288 Chirality : 0.044 0.164 764 Planarity : 0.004 0.037 881 Dihedral : 4.569 20.818 727 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.73 % Allowed : 14.13 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 are not related in a simple way. whole: 0.16 (0.34), residues: 629 helix: -2.05 (0.82), residues: 34 sheet: 0.88 (0.36), residues: 224 loop : -0.11 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.020 0.001 TYR A 369 PHE 0.011 0.001 PHE H 78 TRP 0.015 0.001 TRP L 189 HIS 0.001 0.000 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5029) covalent geometry : angle 0.55465 ( 6863) SS BOND : bond 0.00202 ( 8) SS BOND : angle 0.49361 ( 16) hydrogen bonds : bond 0.03101 ( 181) hydrogen bonds : angle 5.44228 ( 486) link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 1.40206 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.75 seconds wall clock time: 29 minutes 34.67 seconds (1774.67 seconds total)