Starting phenix.real_space_refine on Wed Sep 17 05:33:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eaj_47833/09_2025/9eaj_47833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eaj_47833/09_2025/9eaj_47833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eaj_47833/09_2025/9eaj_47833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eaj_47833/09_2025/9eaj_47833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eaj_47833/09_2025/9eaj_47833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eaj_47833/09_2025/9eaj_47833.map" } resolution = 3.2 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= 0.000 sd= 0.009 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 24 5.16 5 C 3432 2.51 5 N 843 2.21 5 O 947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 5246 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2906 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 13, 'TRANS': 351} Chain breaks: 3 Chain: "B" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 561 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain breaks: 4 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 835 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 1.42, per 1000 atoms: 0.27 Number of scatterers: 5246 At special positions: 0 Unit cell: (64.74, 97.11, 138.61, 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 24 16.00 O 947 8.00 N 843 7.00 C 3432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " 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 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 189.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 50.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.714A pdb=" N SER A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 90 removed outlier: 3.744A pdb=" N THR A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.533A pdb=" N MET A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 132 removed outlier: 3.539A pdb=" N CYS A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 204 through 244 Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.704A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 306 removed outlier: 4.185A pdb=" N HIS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.008A pdb=" N ASN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 1236 removed outlier: 3.514A pdb=" N LYS A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A1235 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1268 removed outlier: 3.540A pdb=" N LYS A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) Proline residue: A1255 - end of helix Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1283 through 1292 removed outlier: 3.627A pdb=" N TYR A1292 " --> pdb=" O ILE A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1306 removed outlier: 3.786A pdb=" N LEU A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Proline residue: A1299 - end of helix removed outlier: 3.954A pdb=" N TYR A1302 " --> pdb=" O ASN A1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.689A pdb=" N TRP C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.156A pdb=" N VAL D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 8.165A pdb=" N VAL B 109 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 182 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.545A pdb=" N TRP B 35 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET B 33 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.582A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.411A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 14 314 hydrogen bonds defined for protein. 891 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: 0.87 Time building geometry restraints manager: 0.57 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: 1574 1.34 - 1.45: 946 1.45 - 1.57: 2819 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5375 Sorted by residual: bond pdb=" CB TRP A 232 " pdb=" CG TRP A 232 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.62e-01 bond pdb=" CG LEU A 319 " pdb=" CD1 LEU A 319 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.36e-01 bond pdb=" CB MET A 258 " pdb=" CG MET A 258 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.62e-01 bond pdb=" CB TRP C 102 " pdb=" CG TRP C 102 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.41e-01 bond pdb=" CE2 PHE C 114 " pdb=" CZ PHE C 114 " ideal model delta sigma weight residual 1.382 1.358 0.024 3.00e-02 1.11e+03 6.25e-01 ... (remaining 5370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 7204 1.63 - 3.26: 77 3.26 - 4.89: 13 4.89 - 6.52: 7 6.52 - 8.15: 1 Bond angle restraints: 7302 Sorted by residual: angle pdb=" CA TRP A 232 " pdb=" CB TRP A 232 " pdb=" CG TRP A 232 " ideal model delta sigma weight residual 113.60 108.51 5.09 1.90e+00 2.77e-01 7.18e+00 angle pdb=" CA LEU A 319 " pdb=" CB LEU A 319 " pdb=" CG LEU A 319 " ideal model delta sigma weight residual 116.30 124.45 -8.15 3.50e+00 8.16e-02 5.42e+00 angle pdb=" CA TYR D 50 " pdb=" CB TYR D 50 " pdb=" CG TYR D 50 " ideal model delta sigma weight residual 113.90 117.64 -3.74 1.80e+00 3.09e-01 4.32e+00 angle pdb=" N SER D 51 " pdb=" CA SER D 51 " pdb=" C SER D 51 " ideal model delta sigma weight residual 109.79 106.87 2.92 1.56e+00 4.11e-01 3.51e+00 angle pdb=" C ASN A 231 " pdb=" N TRP A 232 " pdb=" CA TRP A 232 " ideal model delta sigma weight residual 120.31 117.53 2.78 1.52e+00 4.33e-01 3.35e+00 ... (remaining 7297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2922 17.92 - 35.85: 164 35.85 - 53.77: 32 53.77 - 71.69: 9 71.69 - 89.62: 3 Dihedral angle restraints: 3130 sinusoidal: 1193 harmonic: 1937 Sorted by residual: dihedral pdb=" N ASN A 168 " pdb=" CA ASN A 168 " pdb=" CB ASN A 168 " pdb=" CG ASN A 168 " ideal model delta sinusoidal sigma weight residual -60.00 -119.35 59.35 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG D 25 " pdb=" CA ARG D 25 " pdb=" CB ARG D 25 " pdb=" CG ARG D 25 " ideal model delta sinusoidal sigma weight residual -180.00 -124.79 -55.21 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" CB GLU B 45 " pdb=" CG GLU B 45 " pdb=" CD GLU B 45 " pdb=" OE1 GLU B 45 " ideal model delta sinusoidal sigma weight residual 0.00 80.58 -80.58 1 3.00e+01 1.11e-03 8.92e+00 ... (remaining 3127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 479 0.029 - 0.057: 241 0.057 - 0.086: 73 0.086 - 0.114: 28 0.114 - 0.143: 5 Chirality restraints: 826 Sorted by residual: chirality pdb=" CA TYR D 50 " pdb=" N TYR D 50 " pdb=" C TYR D 50 " pdb=" CB TYR D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL C 40 " pdb=" N VAL C 40 " pdb=" C VAL C 40 " pdb=" CB VAL C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 823 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 108 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO C 109 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 232 " 0.013 2.00e-02 2.50e+03 8.19e-03 1.68e+00 pdb=" CG TRP A 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 232 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 232 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 232 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 232 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 95 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.018 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 102 2.69 - 3.24: 5149 3.24 - 3.79: 8376 3.79 - 4.35: 11151 4.35 - 4.90: 18915 Nonbonded interactions: 43693 Sorted by model distance: nonbonded pdb=" OE1 GLN D 91 " pdb=" OG1 THR D 99 " model vdw 2.136 3.040 nonbonded pdb=" O TYR D 50 " pdb=" OH TYR D 92 " model vdw 2.163 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 104 " model vdw 2.211 3.040 nonbonded pdb=" O THR A 234 " pdb=" ND2 ASN A 238 " model vdw 2.243 3.120 nonbonded pdb=" OH TYR D 37 " pdb=" OE1 GLN D 90 " model vdw 2.253 3.040 ... (remaining 43688 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: 2.960 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.610 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 0.034 5378 Z= 0.170 Angle : 0.512 8.148 7308 Z= 0.266 Chirality : 0.039 0.143 826 Planarity : 0.004 0.051 898 Dihedral : 12.003 89.617 1877 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.78 % Allowed : 7.66 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.76 (0.34), residues: 640 helix: 1.94 (0.29), residues: 296 sheet: -0.46 (0.47), residues: 125 loop : -0.86 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.020 0.001 TYR D 50 PHE 0.014 0.002 PHE A 286 TRP 0.022 0.002 TRP A 232 HIS 0.002 0.000 HIS A1256 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5375) covalent geometry : angle 0.51195 ( 7302) SS BOND : bond 0.00379 ( 3) SS BOND : angle 0.86238 ( 6) hydrogen bonds : bond 0.14101 ( 309) hydrogen bonds : angle 6.37994 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.197 Fit side-chains REVERT: A 93 ARG cc_start: 0.6909 (ptp-170) cc_final: 0.6641 (ptp-170) REVERT: A 175 THR cc_start: 0.7514 (p) cc_final: 0.7295 (p) REVERT: A 190 THR cc_start: 0.7286 (p) cc_final: 0.6914 (m) REVERT: D 46 LYS cc_start: 0.8329 (mttt) cc_final: 0.7951 (ttpp) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.0594 time to fit residues: 7.5539 Evaluate side-chains 79 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN C 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.197282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140356 restraints weight = 6017.970| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.67 r_work: 0.3357 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5378 Z= 0.156 Angle : 0.542 8.321 7308 Z= 0.281 Chirality : 0.040 0.142 826 Planarity : 0.004 0.051 898 Dihedral : 5.470 84.019 725 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.32 % Allowed : 11.05 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.34), residues: 640 helix: 2.21 (0.30), residues: 298 sheet: -0.31 (0.47), residues: 125 loop : -0.75 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.017 0.001 TYR D 50 PHE 0.019 0.002 PHE B 46 TRP 0.021 0.002 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5375) covalent geometry : angle 0.54190 ( 7302) SS BOND : bond 0.00512 ( 3) SS BOND : angle 0.75411 ( 6) hydrogen bonds : bond 0.05083 ( 309) hydrogen bonds : angle 4.80082 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.201 Fit side-chains REVERT: D 46 LYS cc_start: 0.8489 (mttt) cc_final: 0.8143 (tttm) outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 0.0595 time to fit residues: 7.4366 Evaluate side-chains 83 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.198852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142345 restraints weight = 5977.898| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.66 r_work: 0.3368 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5378 Z= 0.130 Angle : 0.505 8.290 7308 Z= 0.260 Chirality : 0.038 0.142 826 Planarity : 0.004 0.050 898 Dihedral : 5.209 82.108 721 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.60 % Allowed : 13.73 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.11 (0.35), residues: 640 helix: 2.21 (0.30), residues: 300 sheet: -0.28 (0.50), residues: 117 loop : -0.71 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.014 0.001 TYR D 50 PHE 0.013 0.001 PHE B 46 TRP 0.019 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5375) covalent geometry : angle 0.50484 ( 7302) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.73550 ( 6) hydrogen bonds : bond 0.04573 ( 309) hydrogen bonds : angle 4.49105 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.192 Fit side-chains REVERT: A 200 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8226 (m110) REVERT: A 243 GLU cc_start: 0.8070 (tp30) cc_final: 0.7717 (tt0) REVERT: D 46 LYS cc_start: 0.8464 (mttt) cc_final: 0.8100 (tttm) REVERT: D 105 LYS cc_start: 0.7124 (ptmt) cc_final: 0.6557 (ttmm) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.0646 time to fit residues: 7.7739 Evaluate side-chains 85 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.197808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141562 restraints weight = 5978.616| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.60 r_work: 0.3357 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5378 Z= 0.148 Angle : 0.517 9.534 7308 Z= 0.265 Chirality : 0.039 0.139 826 Planarity : 0.004 0.051 898 Dihedral : 5.217 81.960 721 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 12.30 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.10 (0.34), residues: 640 helix: 2.22 (0.30), residues: 300 sheet: -0.31 (0.50), residues: 117 loop : -0.72 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.017 0.001 TYR D 50 PHE 0.014 0.001 PHE A 286 TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5375) covalent geometry : angle 0.51704 ( 7302) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.72350 ( 6) hydrogen bonds : bond 0.04603 ( 309) hydrogen bonds : angle 4.38061 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.200 Fit side-chains REVERT: D 46 LYS cc_start: 0.8481 (mttt) cc_final: 0.8101 (tttm) REVERT: D 105 LYS cc_start: 0.7240 (ptmt) cc_final: 0.6692 (ttmm) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.0639 time to fit residues: 8.1198 Evaluate side-chains 91 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.197170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140364 restraints weight = 6094.190| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.67 r_work: 0.3353 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5378 Z= 0.154 Angle : 0.523 8.446 7308 Z= 0.268 Chirality : 0.040 0.135 826 Planarity : 0.004 0.052 898 Dihedral : 5.218 81.669 721 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.39 % Allowed : 13.37 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.04 (0.34), residues: 640 helix: 2.19 (0.30), residues: 300 sheet: -0.36 (0.50), residues: 117 loop : -0.78 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 323 TYR 0.017 0.001 TYR D 50 PHE 0.025 0.002 PHE A1248 TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5375) covalent geometry : angle 0.52234 ( 7302) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.75575 ( 6) hydrogen bonds : bond 0.04598 ( 309) hydrogen bonds : angle 4.36155 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.8535 (mttt) cc_final: 0.8132 (tttm) REVERT: D 105 LYS cc_start: 0.7248 (ptmt) cc_final: 0.6793 (ttmm) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.0603 time to fit residues: 7.9956 Evaluate side-chains 93 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1267 GLN C 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.197432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140337 restraints weight = 6077.148| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.69 r_work: 0.3341 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5378 Z= 0.150 Angle : 0.527 9.094 7308 Z= 0.268 Chirality : 0.039 0.143 826 Planarity : 0.004 0.052 898 Dihedral : 5.223 81.508 721 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.03 % Allowed : 14.08 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.34), residues: 640 helix: 2.22 (0.30), residues: 300 sheet: -0.37 (0.50), residues: 117 loop : -0.74 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.017 0.001 TYR D 50 PHE 0.013 0.001 PHE A 286 TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5375) covalent geometry : angle 0.52657 ( 7302) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.83432 ( 6) hydrogen bonds : bond 0.04534 ( 309) hydrogen bonds : angle 4.33784 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: C 70 ARG cc_start: 0.8697 (mtp180) cc_final: 0.8385 (mtp180) REVERT: D 46 LYS cc_start: 0.8529 (mttt) cc_final: 0.8109 (tttm) REVERT: D 105 LYS cc_start: 0.7240 (ptmt) cc_final: 0.6802 (ttmm) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.0530 time to fit residues: 6.9091 Evaluate side-chains 93 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.197673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140555 restraints weight = 6032.977| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.68 r_work: 0.3353 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5378 Z= 0.149 Angle : 0.528 9.818 7308 Z= 0.267 Chirality : 0.039 0.131 826 Planarity : 0.004 0.053 898 Dihedral : 5.222 81.635 721 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.39 % Allowed : 14.26 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.11 (0.34), residues: 640 helix: 2.25 (0.30), residues: 300 sheet: -0.39 (0.50), residues: 117 loop : -0.72 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 323 TYR 0.018 0.001 TYR D 50 PHE 0.023 0.002 PHE A1248 TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5375) covalent geometry : angle 0.52775 ( 7302) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.77789 ( 6) hydrogen bonds : bond 0.04517 ( 309) hydrogen bonds : angle 4.32705 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8172 (m110) REVERT: D 46 LYS cc_start: 0.8529 (mttt) cc_final: 0.8116 (tttm) REVERT: D 105 LYS cc_start: 0.7232 (ptmt) cc_final: 0.6909 (ttmm) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.0568 time to fit residues: 7.6309 Evaluate side-chains 97 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.0060 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.199191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142514 restraints weight = 5958.932| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.66 r_work: 0.3376 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5378 Z= 0.129 Angle : 0.522 10.616 7308 Z= 0.262 Chirality : 0.039 0.140 826 Planarity : 0.004 0.054 898 Dihedral : 5.215 81.842 721 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 14.80 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.18 (0.35), residues: 640 helix: 2.36 (0.30), residues: 300 sheet: -0.42 (0.49), residues: 119 loop : -0.71 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 323 TYR 0.016 0.001 TYR D 50 PHE 0.014 0.001 PHE A1248 TRP 0.020 0.001 TRP A 232 HIS 0.002 0.000 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5375) covalent geometry : angle 0.52185 ( 7302) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.75704 ( 6) hydrogen bonds : bond 0.04311 ( 309) hydrogen bonds : angle 4.27146 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8120 (m110) REVERT: D 46 LYS cc_start: 0.8537 (mttt) cc_final: 0.8294 (mtpp) REVERT: D 105 LYS cc_start: 0.7167 (ptmt) cc_final: 0.6926 (ttmm) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.0603 time to fit residues: 7.6615 Evaluate side-chains 94 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.198069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141783 restraints weight = 5915.550| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.61 r_work: 0.3339 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5378 Z= 0.133 Angle : 0.514 7.662 7308 Z= 0.262 Chirality : 0.039 0.141 826 Planarity : 0.004 0.053 898 Dihedral : 5.214 81.979 721 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 14.80 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.18 (0.35), residues: 640 helix: 2.35 (0.30), residues: 300 sheet: -0.40 (0.51), residues: 111 loop : -0.70 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.015 0.001 TYR D 50 PHE 0.013 0.001 PHE A 290 TRP 0.021 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5375) covalent geometry : angle 0.51402 ( 7302) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.89650 ( 6) hydrogen bonds : bond 0.04340 ( 309) hydrogen bonds : angle 4.29932 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8119 (m110) REVERT: D 46 LYS cc_start: 0.8510 (mttt) cc_final: 0.8275 (mtpp) outliers start: 15 outliers final: 14 residues processed: 92 average time/residue: 0.0575 time to fit residues: 7.4932 Evaluate side-chains 94 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.198471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142040 restraints weight = 5965.931| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.61 r_work: 0.3376 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5378 Z= 0.133 Angle : 0.515 7.800 7308 Z= 0.262 Chirality : 0.040 0.141 826 Planarity : 0.004 0.054 898 Dihedral : 5.226 81.977 721 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.85 % Allowed : 14.80 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.22 (0.35), residues: 640 helix: 2.40 (0.30), residues: 298 sheet: -0.40 (0.51), residues: 111 loop : -0.69 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.015 0.001 TYR D 50 PHE 0.013 0.001 PHE A 286 TRP 0.021 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5375) covalent geometry : angle 0.51473 ( 7302) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.90362 ( 6) hydrogen bonds : bond 0.04308 ( 309) hydrogen bonds : angle 4.28752 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (m110) REVERT: B 57 ASN cc_start: 0.7856 (p0) cc_final: 0.7651 (p0) REVERT: D 46 LYS cc_start: 0.8525 (mttt) cc_final: 0.8125 (tttm) outliers start: 16 outliers final: 15 residues processed: 90 average time/residue: 0.0623 time to fit residues: 7.8326 Evaluate side-chains 96 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139776 restraints weight = 6013.021| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.64 r_work: 0.3350 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5378 Z= 0.174 Angle : 0.546 7.602 7308 Z= 0.279 Chirality : 0.041 0.148 826 Planarity : 0.004 0.053 898 Dihedral : 5.286 82.033 721 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.85 % Allowed : 14.80 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.07 (0.34), residues: 640 helix: 2.21 (0.30), residues: 300 sheet: -0.41 (0.52), residues: 111 loop : -0.71 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 62 TYR 0.020 0.001 TYR D 50 PHE 0.014 0.002 PHE A 290 TRP 0.021 0.002 TRP A 232 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5375) covalent geometry : angle 0.54505 ( 7302) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.23965 ( 6) hydrogen bonds : bond 0.04660 ( 309) hydrogen bonds : angle 4.37514 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.32 seconds wall clock time: 28 minutes 23.91 seconds (1703.91 seconds total)