Starting phenix.real_space_refine on Wed Jul 1 23:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jcv_61377/07_2026/9jcv_61377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jcv_61377/07_2026/9jcv_61377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jcv_61377/07_2026/9jcv_61377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jcv_61377/07_2026/9jcv_61377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jcv_61377/07_2026/9jcv_61377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jcv_61377/07_2026/9jcv_61377.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.079 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 2756 2.51 5 N 617 2.21 5 O 705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4111 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4068 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.12, per 1000 atoms: 0.27 Number of scatterers: 4111 At special positions: 0 Unit cell: (80.152, 68.036, 84.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 705 8.00 N 617 7.00 C 2756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 163 " " NAG A 702 " - " ASN A 179 " " NAG A 703 " - " ASN A 190 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 146.6 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 930 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 79.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.662A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Proline residue: A 68 - end of helix removed outlier: 4.202A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 105 removed outlier: 3.551A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 6.084A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.980A pdb=" N ILE A 116 " --> pdb=" O CYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.163A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 218 through 238 removed outlier: 3.952A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 266 removed outlier: 3.709A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.913A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.473A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.821A pdb=" N GLY A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.067A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 368 through 381 Proline residue: A 375 - end of helix removed outlier: 3.881A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.620A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 445 through 448 removed outlier: 4.008A pdb=" N THR A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.980A pdb=" N ALA A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.621A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.685A pdb=" N GLN A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.580A pdb=" N TYR A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 257 hydrogen bonds defined for protein. 756 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: 0.57 Time building geometry restraints manager: 0.47 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: 1143 1.34 - 1.46: 897 1.46 - 1.58: 2157 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 4243 Sorted by residual: bond pdb=" N THR A 105 " pdb=" CA THR A 105 " ideal model delta sigma weight residual 1.457 1.423 0.034 1.23e-02 6.61e+03 7.81e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" CA THR A 105 " pdb=" CB THR A 105 " ideal model delta sigma weight residual 1.529 1.503 0.025 1.34e-02 5.57e+03 3.61e+00 bond pdb=" C TYR A 104 " pdb=" N THR A 105 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.46e-02 4.69e+03 2.85e+00 bond pdb=" C THR A 105 " pdb=" O THR A 105 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.22e-02 6.72e+03 2.53e+00 ... (remaining 4238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 5631 1.61 - 3.22: 119 3.22 - 4.83: 27 4.83 - 6.44: 7 6.44 - 8.05: 2 Bond angle restraints: 5786 Sorted by residual: angle pdb=" C TYR A 104 " pdb=" N THR A 105 " pdb=" CA THR A 105 " ideal model delta sigma weight residual 122.77 117.44 5.33 1.33e+00 5.65e-01 1.60e+01 angle pdb=" N PHE A 404 " pdb=" CA PHE A 404 " pdb=" CB PHE A 404 " ideal model delta sigma weight residual 110.12 114.41 -4.29 1.47e+00 4.63e-01 8.52e+00 angle pdb=" N VAL A 405 " pdb=" CA VAL A 405 " pdb=" CB VAL A 405 " ideal model delta sigma weight residual 110.58 114.85 -4.27 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 122.54 117.88 4.66 1.65e+00 3.67e-01 7.99e+00 angle pdb=" CB MET A 176 " pdb=" CG MET A 176 " pdb=" SD MET A 176 " ideal model delta sigma weight residual 112.70 120.75 -8.05 3.00e+00 1.11e-01 7.21e+00 ... (remaining 5781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 2194 17.42 - 34.85: 181 34.85 - 52.27: 45 52.27 - 69.69: 2 69.69 - 87.12: 4 Dihedral angle restraints: 2426 sinusoidal: 954 harmonic: 1472 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -124.02 38.02 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP A 494 " pdb=" CB ASP A 494 " pdb=" CG ASP A 494 " pdb=" OD1 ASP A 494 " ideal model delta sinusoidal sigma weight residual -30.00 -81.99 51.99 1 2.00e+01 2.50e-03 9.22e+00 ... (remaining 2423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 512 0.050 - 0.100: 111 0.100 - 0.150: 20 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 647 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL A 447 " pdb=" CA VAL A 447 " pdb=" CG1 VAL A 447 " pdb=" CG2 VAL A 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA THR A 105 " pdb=" N THR A 105 " pdb=" C THR A 105 " pdb=" CB THR A 105 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 644 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 404 " 0.013 2.00e-02 2.50e+03 2.05e-02 7.33e+00 pdb=" CG PHE A 404 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 404 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 404 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 404 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 404 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 404 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 400 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C LEU A 400 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 400 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 401 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU A 87 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 87 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 88 " -0.010 2.00e-02 2.50e+03 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 985 2.78 - 3.31: 4105 3.31 - 3.84: 6930 3.84 - 4.37: 7600 4.37 - 4.90: 13583 Nonbonded interactions: 33203 Sorted by model distance: nonbonded pdb=" ND2 ASN A 74 " pdb=" OD2 ASP A 293 " model vdw 2.250 3.120 nonbonded pdb=" OH TYR A 72 " pdb=" O ILE A 359 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A 207 " pdb=" O GLY A 209 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A 531 " pdb=" O TYR A 536 " model vdw 2.280 3.040 nonbonded pdb=" OE2 GLU A 197 " pdb=" NH1 ARG A 201 " model vdw 2.288 3.120 ... (remaining 33198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.600 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.470 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 0.040 4247 Z= 0.160 Angle : 0.630 8.477 5797 Z= 0.329 Chirality : 0.044 0.250 647 Planarity : 0.004 0.036 700 Dihedral : 13.635 87.115 1493 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.38), residues: 508 helix: 1.24 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -0.33 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 263 TYR 0.019 0.001 TYR A 489 PHE 0.046 0.002 PHE A 404 TRP 0.016 0.001 TRP A 236 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 ( 4243) covalent geometry : angle 0.61901 / 0.33 ( 5786) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.75052 / 0.41 ( 2) hydrogen bonds : bond 0.11066 / 7.51 ( 257) hydrogen bonds : angle 4.85607 / 3.46 ( 756) link_NAG-ASN : bond 0.00802 / 0.42 ( 3) link_NAG-ASN : angle 3.03075 / 1.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.151 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0630 time to fit residues: 7.6021 Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.199523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.162149 restraints weight = 5001.364| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.21 r_work: 0.3838 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4247 Z= 0.116 Angle : 0.577 8.689 5797 Z= 0.290 Chirality : 0.043 0.328 647 Planarity : 0.004 0.036 700 Dihedral : 4.734 52.930 617 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.23 % Allowed : 7.57 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.38), residues: 508 helix: 1.49 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -0.63 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.014 0.001 TYR A 137 PHE 0.023 0.002 PHE A 391 TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 4243) covalent geometry : angle 0.56349 / 0.29 ( 5786) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.75056 / 0.42 ( 2) hydrogen bonds : bond 0.03750 / 2.44 ( 257) hydrogen bonds : angle 4.14112 / 2.93 ( 756) link_NAG-ASN : bond 0.00883 / 0.46 ( 3) link_NAG-ASN : angle 3.13424 / 1.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 538 TYR cc_start: 0.8125 (m-10) cc_final: 0.7746 (m-80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0591 time to fit residues: 7.0042 Evaluate side-chains 74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.200148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163248 restraints weight = 5071.619| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.09 r_work: 0.3866 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4247 Z= 0.127 Angle : 0.581 8.624 5797 Z= 0.290 Chirality : 0.043 0.312 647 Planarity : 0.004 0.035 700 Dihedral : 4.681 53.039 617 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.92 % Allowed : 11.47 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.37), residues: 508 helix: 1.50 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.014 0.001 TYR A 532 PHE 0.034 0.002 PHE A 522 TRP 0.009 0.001 TRP A 236 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 4243) covalent geometry : angle 0.56821 / 0.29 ( 5786) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.75454 / 0.41 ( 2) hydrogen bonds : bond 0.03782 / 2.43 ( 257) hydrogen bonds : angle 4.23169 / 2.99 ( 756) link_NAG-ASN : bond 0.00874 / 0.46 ( 3) link_NAG-ASN : angle 3.10420 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 266 THR cc_start: 0.8377 (t) cc_final: 0.8125 (p) REVERT: A 403 GLN cc_start: 0.7511 (tp-100) cc_final: 0.6944 (mm-40) REVERT: A 522 PHE cc_start: 0.6821 (t80) cc_final: 0.5972 (m-80) REVERT: A 538 TYR cc_start: 0.8145 (m-10) cc_final: 0.7787 (m-80) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.0603 time to fit residues: 7.0503 Evaluate side-chains 77 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.197483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160870 restraints weight = 4999.635| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.98 r_work: 0.3837 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4247 Z= 0.143 Angle : 0.626 8.697 5797 Z= 0.304 Chirality : 0.043 0.306 647 Planarity : 0.004 0.033 700 Dihedral : 4.660 53.050 617 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.92 % Allowed : 13.07 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.37), residues: 508 helix: 1.42 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.77 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.014 0.001 TYR A 137 PHE 0.031 0.002 PHE A 522 TRP 0.012 0.001 TRP A 236 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4243) covalent geometry : angle 0.61483 / 0.30 ( 5786) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.73575 / 0.40 ( 2) hydrogen bonds : bond 0.03901 / 2.53 ( 257) hydrogen bonds : angle 4.39017 / 3.10 ( 756) link_NAG-ASN : bond 0.00868 / 0.46 ( 3) link_NAG-ASN : angle 3.09093 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.6760 (m-80) cc_final: 0.6378 (t80) REVERT: A 309 MET cc_start: 0.8178 (mmt) cc_final: 0.7929 (mmt) REVERT: A 429 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 446 MET cc_start: 0.8714 (ptp) cc_final: 0.8368 (ptp) REVERT: A 538 TYR cc_start: 0.8214 (m-10) cc_final: 0.7745 (m-80) outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.0446 time to fit residues: 5.2042 Evaluate side-chains 76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.199155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163970 restraints weight = 4994.992| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.00 r_work: 0.3892 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4247 Z= 0.128 Angle : 0.611 10.032 5797 Z= 0.294 Chirality : 0.042 0.304 647 Planarity : 0.004 0.032 700 Dihedral : 4.633 53.207 617 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.69 % Allowed : 15.37 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.38), residues: 508 helix: 1.50 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.63 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 284 TYR 0.015 0.001 TYR A 137 PHE 0.030 0.001 PHE A 522 TRP 0.013 0.001 TRP A 236 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4243) covalent geometry : angle 0.59919 / 0.29 ( 5786) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.71477 / 0.39 ( 2) hydrogen bonds : bond 0.03758 / 2.43 ( 257) hydrogen bonds : angle 4.33545 / 3.05 ( 756) link_NAG-ASN : bond 0.00855 / 0.45 ( 3) link_NAG-ASN : angle 3.09372 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.8217 (mmt) cc_final: 0.7946 (mmt) REVERT: A 446 MET cc_start: 0.8761 (ptp) cc_final: 0.8437 (ptp) REVERT: A 494 ASP cc_start: 0.7920 (m-30) cc_final: 0.7440 (m-30) REVERT: A 522 PHE cc_start: 0.7489 (t80) cc_final: 0.6171 (m-80) REVERT: A 538 TYR cc_start: 0.8209 (m-10) cc_final: 0.7785 (m-80) outliers start: 3 outliers final: 2 residues processed: 86 average time/residue: 0.0516 time to fit residues: 6.1173 Evaluate side-chains 76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.198302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.163467 restraints weight = 5074.131| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.97 r_work: 0.3878 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4247 Z= 0.136 Angle : 0.633 9.854 5797 Z= 0.307 Chirality : 0.044 0.302 647 Planarity : 0.004 0.032 700 Dihedral : 4.685 53.191 617 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.46 % Allowed : 16.51 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.37), residues: 508 helix: 1.37 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.71 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 427 TYR 0.015 0.001 TYR A 536 PHE 0.048 0.002 PHE A 404 TRP 0.018 0.001 TRP A 236 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4243) covalent geometry : angle 0.62132 / 0.30 ( 5786) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.70547 / 0.38 ( 2) hydrogen bonds : bond 0.03827 / 2.47 ( 257) hydrogen bonds : angle 4.44231 / 3.13 ( 756) link_NAG-ASN : bond 0.00859 / 0.45 ( 3) link_NAG-ASN : angle 3.09562 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.6567 (m-80) cc_final: 0.6347 (t80) REVERT: A 178 LYS cc_start: 0.7591 (mmtt) cc_final: 0.7334 (mmtt) REVERT: A 309 MET cc_start: 0.8256 (mmt) cc_final: 0.7926 (mmt) REVERT: A 494 ASP cc_start: 0.7870 (m-30) cc_final: 0.7375 (m-30) REVERT: A 522 PHE cc_start: 0.7394 (t80) cc_final: 0.6183 (m-80) REVERT: A 538 TYR cc_start: 0.8215 (m-10) cc_final: 0.7716 (m-80) outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.0580 time to fit residues: 6.1289 Evaluate side-chains 76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.199278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163620 restraints weight = 5043.318| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.02 r_work: 0.3878 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4247 Z= 0.132 Angle : 0.632 10.675 5797 Z= 0.304 Chirality : 0.044 0.301 647 Planarity : 0.004 0.032 700 Dihedral : 4.678 53.271 617 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.69 % Allowed : 16.51 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.38), residues: 508 helix: 1.42 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.67 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.015 0.001 TYR A 137 PHE 0.036 0.002 PHE A 404 TRP 0.017 0.001 TRP A 236 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4243) covalent geometry : angle 0.62076 / 0.30 ( 5786) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.72529 / 0.40 ( 2) hydrogen bonds : bond 0.03831 / 2.48 ( 257) hydrogen bonds : angle 4.36989 / 3.07 ( 756) link_NAG-ASN : bond 0.00863 / 0.45 ( 3) link_NAG-ASN : angle 3.08715 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.6591 (m-80) cc_final: 0.6389 (t80) REVERT: A 309 MET cc_start: 0.8273 (mmt) cc_final: 0.7958 (mmt) REVERT: A 446 MET cc_start: 0.8657 (ptp) cc_final: 0.8329 (ptp) REVERT: A 494 ASP cc_start: 0.7911 (m-30) cc_final: 0.7422 (m-30) REVERT: A 504 MET cc_start: 0.5623 (ttm) cc_final: 0.5370 (ttm) REVERT: A 522 PHE cc_start: 0.7360 (t80) cc_final: 0.6214 (m-80) REVERT: A 538 TYR cc_start: 0.8214 (m-10) cc_final: 0.7680 (m-80) outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 0.0554 time to fit residues: 6.0225 Evaluate side-chains 76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.198497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162850 restraints weight = 5015.736| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.01 r_work: 0.3873 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4247 Z= 0.141 Angle : 0.658 10.794 5797 Z= 0.316 Chirality : 0.044 0.298 647 Planarity : 0.004 0.033 700 Dihedral : 4.723 53.266 617 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.46 % Allowed : 17.89 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.38), residues: 508 helix: 1.38 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.67 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 428 TYR 0.015 0.001 TYR A 137 PHE 0.037 0.002 PHE A 404 TRP 0.014 0.001 TRP A 236 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4243) covalent geometry : angle 0.64646 / 0.31 ( 5786) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.71914 / 0.39 ( 2) hydrogen bonds : bond 0.03904 / 2.54 ( 257) hydrogen bonds : angle 4.41615 / 3.10 ( 756) link_NAG-ASN : bond 0.00854 / 0.45 ( 3) link_NAG-ASN : angle 3.15564 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.6724 (m-80) cc_final: 0.6405 (t80) REVERT: A 309 MET cc_start: 0.8322 (mmt) cc_final: 0.8065 (mmt) REVERT: A 446 MET cc_start: 0.8645 (ptp) cc_final: 0.8319 (ptp) REVERT: A 494 ASP cc_start: 0.7852 (m-30) cc_final: 0.7379 (m-30) REVERT: A 504 MET cc_start: 0.5666 (ttm) cc_final: 0.5398 (ttm) REVERT: A 522 PHE cc_start: 0.7356 (t80) cc_final: 0.6242 (m-80) REVERT: A 538 TYR cc_start: 0.8252 (m-10) cc_final: 0.7764 (m-80) outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.0513 time to fit residues: 5.5199 Evaluate side-chains 75 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 45 optimal weight: 0.0970 chunk 12 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.199982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165216 restraints weight = 5135.842| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.01 r_work: 0.3898 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4247 Z= 0.125 Angle : 0.642 10.921 5797 Z= 0.311 Chirality : 0.044 0.300 647 Planarity : 0.004 0.033 700 Dihedral : 4.669 53.314 617 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.46 % Allowed : 17.66 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.38), residues: 508 helix: 1.43 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 240 TYR 0.015 0.001 TYR A 137 PHE 0.027 0.002 PHE A 404 TRP 0.009 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4243) covalent geometry : angle 0.63068 / 0.31 ( 5786) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.73616 / 0.40 ( 2) hydrogen bonds : bond 0.03778 / 2.46 ( 257) hydrogen bonds : angle 4.40971 / 3.08 ( 756) link_NAG-ASN : bond 0.00880 / 0.46 ( 3) link_NAG-ASN : angle 3.05461 / 1.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8968 (mp) cc_final: 0.8698 (mp) REVERT: A 309 MET cc_start: 0.8381 (mmt) cc_final: 0.8006 (mmt) REVERT: A 426 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: A 446 MET cc_start: 0.8683 (ptp) cc_final: 0.8379 (ptp) REVERT: A 494 ASP cc_start: 0.7745 (m-30) cc_final: 0.7272 (m-30) REVERT: A 504 MET cc_start: 0.5549 (ttm) cc_final: 0.5318 (ttm) REVERT: A 522 PHE cc_start: 0.7317 (t80) cc_final: 0.6254 (m-80) REVERT: A 538 TYR cc_start: 0.8195 (m-10) cc_final: 0.7741 (m-80) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.0422 time to fit residues: 4.5427 Evaluate side-chains 74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 426 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.199642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.164995 restraints weight = 4965.053| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.94 r_work: 0.3899 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4247 Z= 0.132 Angle : 0.658 11.002 5797 Z= 0.318 Chirality : 0.044 0.299 647 Planarity : 0.004 0.033 700 Dihedral : 4.711 53.268 617 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.69 % Allowed : 19.04 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.38), residues: 508 helix: 1.42 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.59 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.017 0.001 TYR A 536 PHE 0.025 0.002 PHE A 404 TRP 0.010 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4243) covalent geometry : angle 0.64627 / 0.32 ( 5786) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 0.71594 / 0.39 ( 2) hydrogen bonds : bond 0.03797 / 2.48 ( 257) hydrogen bonds : angle 4.40395 / 3.08 ( 756) link_NAG-ASN : bond 0.00865 / 0.45 ( 3) link_NAG-ASN : angle 3.16282 / 1.23 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.8372 (mmt) cc_final: 0.7992 (mmt) REVERT: A 446 MET cc_start: 0.8690 (ptp) cc_final: 0.8393 (ptp) REVERT: A 494 ASP cc_start: 0.7731 (m-30) cc_final: 0.7269 (m-30) REVERT: A 504 MET cc_start: 0.5648 (ttm) cc_final: 0.5391 (ttm) REVERT: A 522 PHE cc_start: 0.7310 (t80) cc_final: 0.6262 (m-80) REVERT: A 538 TYR cc_start: 0.8170 (m-10) cc_final: 0.7650 (m-80) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.0382 time to fit residues: 3.9666 Evaluate side-chains 72 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.196797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162485 restraints weight = 5071.876| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.96 r_work: 0.3868 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4247 Z= 0.153 Angle : 0.678 11.017 5797 Z= 0.328 Chirality : 0.044 0.295 647 Planarity : 0.004 0.034 700 Dihedral : 4.774 53.357 617 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.92 % Allowed : 18.81 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.38), residues: 508 helix: 1.36 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -0.65 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.017 0.001 TYR A 536 PHE 0.027 0.002 PHE A 522 TRP 0.010 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4243) covalent geometry : angle 0.66780 / 0.33 ( 5786) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.72518 / 0.39 ( 2) hydrogen bonds : bond 0.04036 / 2.63 ( 257) hydrogen bonds : angle 4.51910 / 3.16 ( 756) link_NAG-ASN : bond 0.00886 / 0.46 ( 3) link_NAG-ASN : angle 3.02238 / 1.17 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1078.16 seconds wall clock time: 19 minutes 14.86 seconds (1154.86 seconds total)