Starting phenix.real_space_refine on Thu Jun 5 08:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4r_41892/06_2025/8u4r_41892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4r_41892/06_2025/8u4r_41892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4r_41892/06_2025/8u4r_41892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4r_41892/06_2025/8u4r_41892.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4r_41892/06_2025/8u4r_41892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4r_41892/06_2025/8u4r_41892.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2008 atoms to isotropic. 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 23 5.16 5 C 2680 2.51 5 N 676 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4107 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 864 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2239 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.77 Number of scatterers: 4107 At special positions: 0 Unit cell: (55.25, 65.45, 110.5, 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 23 16.00 O 728 8.00 N 676 7.00 C 2680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " 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: 0.92 Conformation dependent library (CDL) restraints added in 438.4 milliseconds 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 7 sheets defined 46.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 65 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 71 through 100 removed outlier: 3.709A pdb=" N LYS R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 106 through 140 removed outlier: 4.133A pdb=" N SER R 123 " --> pdb=" O SER R 119 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE R 126 " --> pdb=" O SER R 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 160 removed outlier: 3.880A pdb=" N VAL R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR R 157 " --> pdb=" O GLU R 153 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 167 Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 209 removed outlier: 4.494A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 226 Processing helix chain 'R' and resid 235 through 252 removed outlier: 3.819A pdb=" N THR R 240 " --> pdb=" O LYS R 236 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP R 252 " --> pdb=" O PHE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 267 Processing helix chain 'R' and resid 274 through 292 Processing helix chain 'R' and resid 293 through 295 No H-bonds generated for 'chain 'R' and resid 293 through 295' Processing helix chain 'R' and resid 296 through 304 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.506A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.327A pdb=" N TYR H 32 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.944A pdb=" N CYS H 96 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL H 115 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG H 98 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR H 111 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N THR H 102 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N TYR H 109 " --> pdb=" O THR H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 175 through 180 243 hydrogen bonds defined for protein. 678 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: 1.09 Time building geometry restraints manager: 1.12 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: 1254 1.34 - 1.46: 1017 1.46 - 1.58: 1910 1.58 - 1.70: 1 1.70 - 1.82: 33 Bond restraints: 4215 Sorted by residual: bond pdb=" C6 CLR R 701 " pdb=" C7 CLR R 701 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C14 CLR R 701 " pdb=" C15 CLR R 701 " ideal model delta sigma weight residual 1.523 1.565 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C13 CLR R 701 " pdb=" C14 CLR R 701 " ideal model delta sigma weight residual 1.537 1.578 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C20 CLR R 701 " pdb=" C22 CLR R 701 " ideal model delta sigma weight residual 1.535 1.575 -0.040 2.00e-02 2.50e+03 4.01e+00 bond pdb=" C15 CLR R 701 " pdb=" C16 CLR R 701 " ideal model delta sigma weight residual 1.541 1.581 -0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 4210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 5526 1.55 - 3.10: 158 3.10 - 4.65: 39 4.65 - 6.20: 10 6.20 - 7.75: 4 Bond angle restraints: 5737 Sorted by residual: angle pdb=" CA TRP H 116 " pdb=" CB TRP H 116 " pdb=" CG TRP H 116 " ideal model delta sigma weight residual 113.60 119.67 -6.07 1.90e+00 2.77e-01 1.02e+01 angle pdb=" C TYR H 111 " pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 123.46 116.30 7.16 2.42e+00 1.71e-01 8.74e+00 angle pdb=" C ASP R 181 " pdb=" CA ASP R 181 " pdb=" CB ASP R 181 " ideal model delta sigma weight residual 110.42 116.07 -5.65 1.99e+00 2.53e-01 8.07e+00 angle pdb=" N LEU L 52 " pdb=" CA LEU L 52 " pdb=" C LEU L 52 " ideal model delta sigma weight residual 112.12 108.44 3.68 1.34e+00 5.57e-01 7.53e+00 angle pdb=" C GLY H 112 " pdb=" N MET H 113 " pdb=" CA MET H 113 " ideal model delta sigma weight residual 123.93 128.07 -4.14 1.54e+00 4.22e-01 7.24e+00 ... (remaining 5732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2254 17.92 - 35.83: 205 35.83 - 53.75: 35 53.75 - 71.67: 4 71.67 - 89.58: 5 Dihedral angle restraints: 2503 sinusoidal: 1011 harmonic: 1492 Sorted by residual: dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual -86.00 -161.73 75.73 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 135.21 -42.21 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " pdb=" CD GLU L 86 " pdb=" OE1 GLU L 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.58 -89.58 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 588 0.074 - 0.148: 55 0.148 - 0.222: 3 0.222 - 0.296: 2 0.296 - 0.371: 2 Chirality restraints: 650 Sorted by residual: chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C20 CLR R 701 " pdb=" C17 CLR R 701 " pdb=" C21 CLR R 701 " pdb=" C22 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -3.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 647 not shown) Planarity restraints: 704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 216 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C LEU R 216 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU R 216 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 217 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 190 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO R 191 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 191 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 191 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 91 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO R 92 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 92 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 92 " 0.034 5.00e-02 4.00e+02 ... (remaining 701 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 103 2.71 - 3.26: 3861 3.26 - 3.81: 6317 3.81 - 4.35: 7782 4.35 - 4.90: 14107 Nonbonded interactions: 32170 Sorted by model distance: nonbonded pdb=" OG1 THR R 117 " pdb=" OD2 ASP R 171 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG L 51 " pdb=" OD1 ASP H 114 " model vdw 2.221 3.120 nonbonded pdb=" OE1 GLN R 200 " pdb=" OG SER R 263 " model vdw 2.313 3.040 nonbonded pdb=" O ALA R 83 " pdb=" OG SER R 119 " model vdw 2.334 3.040 nonbonded pdb=" NH2 ARG H 105 " pdb=" OE1 GLU R 288 " model vdw 2.404 3.120 ... (remaining 32165 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.003 0.050 4219 Z= 0.149 Angle : 0.673 7.746 5745 Z= 0.345 Chirality : 0.050 0.371 650 Planarity : 0.006 0.063 704 Dihedral : 14.014 89.582 1537 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.40), residues: 503 helix: 1.07 (0.38), residues: 218 sheet: 0.04 (0.46), residues: 133 loop : -0.55 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 116 HIS 0.004 0.001 HIS R 294 PHE 0.012 0.001 PHE R 293 TYR 0.010 0.001 TYR H 107 ARG 0.004 0.001 ARG L 51 Details of bonding type rmsd hydrogen bonds : bond 0.13192 ( 231) hydrogen bonds : angle 7.16225 ( 678) SS BOND : bond 0.00378 ( 4) SS BOND : angle 1.31031 ( 8) covalent geometry : bond 0.00311 ( 4215) covalent geometry : angle 0.67157 ( 5737) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.411 Fit side-chains REVERT: R 24 MET cc_start: 0.6356 (tmm) cc_final: 0.6053 (tmm) REVERT: R 301 LEU cc_start: 0.8430 (mp) cc_final: 0.8173 (mp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1984 time to fit residues: 16.0786 Evaluate side-chains 59 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124137 restraints weight = 4653.456| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.69 r_work: 0.3330 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4219 Z= 0.125 Angle : 0.559 5.316 5745 Z= 0.292 Chirality : 0.042 0.139 650 Planarity : 0.005 0.056 704 Dihedral : 4.416 21.593 627 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.45 % Allowed : 5.38 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.39), residues: 503 helix: 1.37 (0.37), residues: 214 sheet: 0.21 (0.47), residues: 133 loop : -0.68 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS R 203 PHE 0.007 0.001 PHE L 41 TYR 0.007 0.001 TYR H 54 ARG 0.003 0.000 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 231) hydrogen bonds : angle 5.11613 ( 678) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.96284 ( 8) covalent geometry : bond 0.00298 ( 4215) covalent geometry : angle 0.55778 ( 5737) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.418 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.2043 time to fit residues: 14.3674 Evaluate side-chains 55 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.0040 chunk 48 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123899 restraints weight = 4645.917| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.67 r_work: 0.3332 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4219 Z= 0.116 Angle : 0.521 5.242 5745 Z= 0.273 Chirality : 0.041 0.136 650 Planarity : 0.005 0.057 704 Dihedral : 4.293 20.360 627 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.67 % Allowed : 7.62 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.39), residues: 503 helix: 1.62 (0.36), residues: 214 sheet: 0.28 (0.46), residues: 134 loop : -0.67 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.008 0.001 TYR H 54 ARG 0.002 0.000 ARG R 235 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 231) hydrogen bonds : angle 4.79910 ( 678) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.82861 ( 8) covalent geometry : bond 0.00279 ( 4215) covalent geometry : angle 0.52045 ( 5737) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.377 Fit side-chains REVERT: L 94 MET cc_start: 0.9179 (ttt) cc_final: 0.8904 (ttp) REVERT: R 28 CYS cc_start: 0.7722 (m) cc_final: 0.7453 (m) REVERT: R 154 LYS cc_start: 0.7607 (mptt) cc_final: 0.6555 (tttm) outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.2157 time to fit residues: 14.9314 Evaluate side-chains 55 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120207 restraints weight = 4736.407| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.72 r_work: 0.3279 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4219 Z= 0.154 Angle : 0.569 5.638 5745 Z= 0.295 Chirality : 0.043 0.145 650 Planarity : 0.005 0.059 704 Dihedral : 4.447 19.825 627 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.45 % Allowed : 10.54 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.39), residues: 503 helix: 1.68 (0.37), residues: 213 sheet: 0.26 (0.46), residues: 133 loop : -0.70 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.002 0.001 HIS H 110 PHE 0.006 0.001 PHE L 41 TYR 0.012 0.001 TYR H 54 ARG 0.002 0.000 ARG L 51 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 231) hydrogen bonds : angle 4.79245 ( 678) SS BOND : bond 0.00386 ( 4) SS BOND : angle 0.83038 ( 8) covalent geometry : bond 0.00384 ( 4215) covalent geometry : angle 0.56862 ( 5737) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.459 Fit side-chains REVERT: R 28 CYS cc_start: 0.7833 (m) cc_final: 0.7602 (m) REVERT: R 154 LYS cc_start: 0.7943 (mptt) cc_final: 0.6871 (tttm) outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.2364 time to fit residues: 17.3130 Evaluate side-chains 60 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.138365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118358 restraints weight = 4922.476| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.74 r_work: 0.3240 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4219 Z= 0.194 Angle : 0.610 5.902 5745 Z= 0.316 Chirality : 0.045 0.150 650 Planarity : 0.005 0.063 704 Dihedral : 4.679 19.783 627 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.02 % Allowed : 11.66 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.39), residues: 503 helix: 1.59 (0.37), residues: 213 sheet: 0.14 (0.47), residues: 133 loop : -0.88 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.003 0.001 HIS H 110 PHE 0.007 0.001 PHE R 199 TYR 0.015 0.001 TYR H 54 ARG 0.005 0.001 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 231) hydrogen bonds : angle 4.87622 ( 678) SS BOND : bond 0.00495 ( 4) SS BOND : angle 0.74884 ( 8) covalent geometry : bond 0.00490 ( 4215) covalent geometry : angle 0.60947 ( 5737) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.399 Fit side-chains REVERT: L 82 ARG cc_start: 0.7554 (mtm110) cc_final: 0.6874 (mtp85) REVERT: L 94 MET cc_start: 0.9232 (ttt) cc_final: 0.8915 (ttp) REVERT: R 154 LYS cc_start: 0.8066 (mptt) cc_final: 0.6916 (tttm) REVERT: R 293 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7640 (t80) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.2218 time to fit residues: 16.2323 Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119684 restraints weight = 4734.660| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.71 r_work: 0.3252 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4219 Z= 0.139 Angle : 0.551 5.635 5745 Z= 0.287 Chirality : 0.042 0.139 650 Planarity : 0.005 0.062 704 Dihedral : 4.485 18.845 627 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.79 % Allowed : 13.23 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.39), residues: 503 helix: 1.65 (0.36), residues: 213 sheet: 0.16 (0.47), residues: 133 loop : -0.86 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.002 0.001 HIS H 110 PHE 0.006 0.001 PHE L 41 TYR 0.010 0.001 TYR H 54 ARG 0.004 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 231) hydrogen bonds : angle 4.75113 ( 678) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.01440 ( 8) covalent geometry : bond 0.00341 ( 4215) covalent geometry : angle 0.55010 ( 5737) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: R 154 LYS cc_start: 0.8094 (mptt) cc_final: 0.6928 (tttm) REVERT: R 171 ASP cc_start: 0.7506 (m-30) cc_final: 0.7157 (m-30) REVERT: R 293 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7651 (t80) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.2254 time to fit residues: 16.1258 Evaluate side-chains 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.142017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122189 restraints weight = 4747.543| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.73 r_work: 0.3285 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4219 Z= 0.110 Angle : 0.514 5.342 5745 Z= 0.268 Chirality : 0.041 0.134 650 Planarity : 0.004 0.062 704 Dihedral : 4.224 17.645 627 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.57 % Allowed : 13.68 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.39), residues: 503 helix: 1.80 (0.36), residues: 213 sheet: 0.17 (0.47), residues: 134 loop : -0.87 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS R 294 PHE 0.006 0.001 PHE L 41 TYR 0.007 0.001 TYR H 54 ARG 0.003 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 231) hydrogen bonds : angle 4.53091 ( 678) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.85834 ( 8) covalent geometry : bond 0.00262 ( 4215) covalent geometry : angle 0.51309 ( 5737) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: R 154 LYS cc_start: 0.8107 (mptt) cc_final: 0.6886 (tttm) REVERT: R 171 ASP cc_start: 0.7487 (m-30) cc_final: 0.7144 (m-30) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.2345 time to fit residues: 17.5173 Evaluate side-chains 62 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117844 restraints weight = 4770.137| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.71 r_work: 0.3254 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4219 Z= 0.181 Angle : 0.598 5.951 5745 Z= 0.310 Chirality : 0.044 0.147 650 Planarity : 0.005 0.062 704 Dihedral : 4.489 17.713 627 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.02 % Allowed : 14.13 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.39), residues: 503 helix: 1.65 (0.37), residues: 213 sheet: 0.12 (0.47), residues: 133 loop : -0.93 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.003 0.001 HIS R 203 PHE 0.007 0.001 PHE R 199 TYR 0.014 0.001 TYR H 54 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 231) hydrogen bonds : angle 4.71471 ( 678) SS BOND : bond 0.00417 ( 4) SS BOND : angle 2.67042 ( 8) covalent geometry : bond 0.00458 ( 4215) covalent geometry : angle 0.58969 ( 5737) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.419 Fit side-chains REVERT: R 154 LYS cc_start: 0.8160 (mptt) cc_final: 0.6931 (tttm) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.2432 time to fit residues: 18.1303 Evaluate side-chains 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120247 restraints weight = 4785.351| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.72 r_work: 0.3257 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4219 Z= 0.129 Angle : 0.546 5.600 5745 Z= 0.284 Chirality : 0.042 0.137 650 Planarity : 0.005 0.062 704 Dihedral : 4.340 16.938 627 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.24 % Allowed : 13.90 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.39), residues: 503 helix: 1.78 (0.36), residues: 213 sheet: 0.14 (0.47), residues: 134 loop : -0.92 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.009 0.001 TYR H 54 ARG 0.006 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 231) hydrogen bonds : angle 4.57092 ( 678) SS BOND : bond 0.00321 ( 4) SS BOND : angle 2.18175 ( 8) covalent geometry : bond 0.00315 ( 4215) covalent geometry : angle 0.53997 ( 5737) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: R 154 LYS cc_start: 0.8096 (mptt) cc_final: 0.6933 (tttm) REVERT: R 171 ASP cc_start: 0.7512 (m-30) cc_final: 0.7182 (m-30) REVERT: R 293 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7636 (t80) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.2665 time to fit residues: 20.1162 Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119720 restraints weight = 4834.980| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.73 r_work: 0.3245 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4219 Z= 0.139 Angle : 0.553 5.706 5745 Z= 0.287 Chirality : 0.042 0.140 650 Planarity : 0.005 0.062 704 Dihedral : 4.341 16.544 627 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.79 % Allowed : 14.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.39), residues: 503 helix: 1.79 (0.36), residues: 213 sheet: 0.12 (0.46), residues: 134 loop : -0.91 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS H 110 PHE 0.006 0.001 PHE L 41 TYR 0.011 0.001 TYR H 54 ARG 0.006 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 231) hydrogen bonds : angle 4.56769 ( 678) SS BOND : bond 0.00344 ( 4) SS BOND : angle 2.07818 ( 8) covalent geometry : bond 0.00347 ( 4215) covalent geometry : angle 0.54791 ( 5737) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: R 154 LYS cc_start: 0.8135 (mptt) cc_final: 0.6921 (tttm) REVERT: R 171 ASP cc_start: 0.7448 (m-30) cc_final: 0.7159 (m-30) REVERT: R 293 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7641 (t80) outliers start: 8 outliers final: 7 residues processed: 58 average time/residue: 0.2622 time to fit residues: 18.7859 Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120612 restraints weight = 4720.835| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.70 r_work: 0.3286 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4219 Z= 0.128 Angle : 0.540 5.555 5745 Z= 0.280 Chirality : 0.042 0.136 650 Planarity : 0.005 0.062 704 Dihedral : 4.276 16.126 627 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.57 % Allowed : 14.80 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.39), residues: 503 helix: 1.85 (0.36), residues: 213 sheet: 0.13 (0.46), residues: 134 loop : -0.87 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS R 203 PHE 0.005 0.001 PHE L 41 TYR 0.009 0.001 TYR H 54 ARG 0.006 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 231) hydrogen bonds : angle 4.52228 ( 678) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.86870 ( 8) covalent geometry : bond 0.00313 ( 4215) covalent geometry : angle 0.53560 ( 5737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.79 seconds wall clock time: 47 minutes 13.66 seconds (2833.66 seconds total)