Starting phenix.real_space_refine on Tue Mar 3 12:36:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7y_33674/03_2026/7y7y_33674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7y_33674/03_2026/7y7y_33674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y7y_33674/03_2026/7y7y_33674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7y_33674/03_2026/7y7y_33674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/03_2026/7y7y_33674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7y_33674/03_2026/7y7y_33674.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.109 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2838 2.51 5 N 650 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4195 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 108 Unusual residues: {' CL': 1, ' NA': 2, 'ID7': 1, 'NAG': 3} Classifications: {'undetermined': 7, 'water': 54} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.10, per 1000 atoms: 0.26 Number of scatterers: 4303 At special positions: 0 Unit cell: (69.28, 71.445, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 778 8.00 N 650 7.00 C 2838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.05 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 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 226.2 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.705A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.690A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.985A pdb=" N VAL A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.950A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 4.136A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.619A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.886A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 315 through 350 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.693A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.162A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.937A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.647A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.402A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 571 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 287 hydrogen bonds defined for protein. 840 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: 0.66 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 622 1.31 - 1.44: 1351 1.44 - 1.56: 2354 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4381 Sorted by residual: bond pdb=" C SER A 456 " pdb=" O SER A 456 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" CA SER A 456 " pdb=" CB SER A 456 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.21e+01 bond pdb=" C1 ID7 A 701 " pdb=" O1 ID7 A 701 " ideal model delta sigma weight residual 1.249 1.198 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 ID7 A 701 " pdb=" O2 ID7 A 701 " ideal model delta sigma weight residual 1.248 1.202 0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 ... (remaining 4376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 5856 2.18 - 4.37: 95 4.37 - 6.55: 14 6.55 - 8.73: 2 8.73 - 10.92: 1 Bond angle restraints: 5968 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.22 -10.92 2.00e+00 2.50e-01 2.98e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.74 -8.24 1.70e+00 3.46e-01 2.35e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.56 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CA ASP A 165 " pdb=" CB ASP A 165 " pdb=" CG ASP A 165 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ALA A 455 " pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 116.22 121.73 -5.51 1.44e+00 4.82e-01 1.46e+01 ... (remaining 5963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2146 17.05 - 34.11: 272 34.11 - 51.16: 75 51.16 - 68.22: 19 68.22 - 85.27: 6 Dihedral angle restraints: 2518 sinusoidal: 999 harmonic: 1519 Sorted by residual: dihedral pdb=" CA PHE A 502 " pdb=" C PHE A 502 " pdb=" N PHE A 503 " pdb=" CA PHE A 503 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -54.23 -31.77 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 662 0.274 - 0.548: 3 0.548 - 0.821: 0 0.821 - 1.095: 0 1.095 - 1.369: 1 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 663 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.008 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" CG ASN A 184 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.191 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.405 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.073 2.00e-02 2.50e+03 7.26e-02 6.60e+01 pdb=" CG ASN A 176 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.116 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.046 2.00e-02 2.50e+03 5.43e-02 3.69e+01 pdb=" CG ASN A 181 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.062 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 31 2.41 - 3.03: 2786 3.03 - 3.66: 6773 3.66 - 4.28: 10892 4.28 - 4.90: 17201 Nonbonded interactions: 37683 Sorted by model distance: nonbonded pdb=" O HOH A 803 " pdb=" O HOH A 822 " model vdw 1.789 3.040 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 805 " model vdw 1.910 3.040 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASP A 287 " pdb=" O HOH A 802 " model vdw 1.987 3.040 nonbonded pdb=" O ALA A 357 " pdb=" O HOH A 803 " model vdw 2.014 3.040 ... (remaining 37678 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.120 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.007 0.271 4385 Z= 0.343 Angle : 0.793 18.529 5979 Z= 0.418 Chirality : 0.072 1.369 666 Planarity : 0.005 0.034 722 Dihedral : 16.872 85.271 1551 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 26.56 % Favored : 72.99 % 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: 0.29 (0.36), residues: 525 helix: 0.73 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.11 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 257 TYR 0.027 0.002 TYR A 72 PHE 0.027 0.003 PHE A 398 TRP 0.017 0.002 TRP A 161 HIS 0.005 0.002 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4381) covalent geometry : angle 0.72532 ( 5968) SS BOND : bond 0.02058 ( 1) SS BOND : angle 6.40781 ( 2) hydrogen bonds : bond 0.13720 ( 287) hydrogen bonds : angle 6.19573 ( 840) link_NAG-ASN : bond 0.16995 ( 3) link_NAG-ASN : angle 7.70618 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.157 Fit side-chains REVERT: A 572 GLN cc_start: 0.7403 (tp40) cc_final: 0.7069 (tt0) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.6127 time to fit residues: 41.1793 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 487 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS A 483 ASN A 534 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.091347 restraints weight = 4229.802| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.37 r_work: 0.2779 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4385 Z= 0.154 Angle : 0.612 7.654 5979 Z= 0.321 Chirality : 0.044 0.223 666 Planarity : 0.004 0.034 722 Dihedral : 5.545 50.680 650 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 22.77 % Favored : 74.33 % 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: 1.00 (0.37), residues: 525 helix: 1.27 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.01 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.022 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4381) covalent geometry : angle 0.59805 ( 5968) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.58898 ( 2) hydrogen bonds : bond 0.06046 ( 287) hydrogen bonds : angle 4.82165 ( 840) link_NAG-ASN : bond 0.00456 ( 3) link_NAG-ASN : angle 3.31121 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.161 Fit side-chains REVERT: A 163 GLN cc_start: 0.8593 (mt0) cc_final: 0.8321 (mt0) REVERT: A 485 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: A 487 MET cc_start: 0.8648 (mtm) cc_final: 0.8446 (mtm) REVERT: A 559 LEU cc_start: 0.7605 (mt) cc_final: 0.7312 (mt) REVERT: A 572 GLN cc_start: 0.7470 (tp40) cc_final: 0.7022 (tt0) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.5527 time to fit residues: 40.1458 Evaluate side-chains 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.089915 restraints weight = 4191.973| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.37 r_work: 0.2770 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4385 Z= 0.181 Angle : 0.645 8.276 5979 Z= 0.337 Chirality : 0.046 0.228 666 Planarity : 0.004 0.036 722 Dihedral : 5.444 52.295 647 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 21.88 % Favored : 75.22 % 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: 1.08 (0.37), residues: 525 helix: 1.36 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.07 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 211 TYR 0.024 0.002 TYR A 72 PHE 0.030 0.003 PHE A 398 TRP 0.017 0.002 TRP A 116 HIS 0.001 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 4381) covalent geometry : angle 0.63218 ( 5968) SS BOND : bond 0.00033 ( 1) SS BOND : angle 5.26082 ( 2) hydrogen bonds : bond 0.06513 ( 287) hydrogen bonds : angle 4.86448 ( 840) link_NAG-ASN : bond 0.00431 ( 3) link_NAG-ASN : angle 2.37348 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.170 Fit side-chains REVERT: A 163 GLN cc_start: 0.8382 (mt0) cc_final: 0.8110 (mt0) REVERT: A 485 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: A 559 LEU cc_start: 0.7743 (mt) cc_final: 0.7431 (mt) REVERT: A 572 GLN cc_start: 0.7463 (tp40) cc_final: 0.7030 (tt0) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.5359 time to fit residues: 39.5272 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.092080 restraints weight = 4172.484| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.36 r_work: 0.2794 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4385 Z= 0.147 Angle : 0.587 7.958 5979 Z= 0.307 Chirality : 0.044 0.202 666 Planarity : 0.004 0.035 722 Dihedral : 5.241 53.499 647 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.12 % Allowed : 21.21 % Favored : 75.67 % 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: 1.27 (0.37), residues: 525 helix: 1.50 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.05 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.023 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4381) covalent geometry : angle 0.57795 ( 5968) SS BOND : bond 0.00134 ( 1) SS BOND : angle 4.02256 ( 2) hydrogen bonds : bond 0.05732 ( 287) hydrogen bonds : angle 4.67525 ( 840) link_NAG-ASN : bond 0.00359 ( 3) link_NAG-ASN : angle 2.04226 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.164 Fit side-chains REVERT: A 163 GLN cc_start: 0.8338 (mt0) cc_final: 0.8099 (mt0) REVERT: A 348 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8288 (t) REVERT: A 487 MET cc_start: 0.8593 (mtm) cc_final: 0.8358 (mtm) REVERT: A 559 LEU cc_start: 0.7874 (mt) cc_final: 0.7504 (mt) REVERT: A 572 GLN cc_start: 0.7485 (tp40) cc_final: 0.7040 (tt0) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.5469 time to fit residues: 40.9464 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.0060 chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 overall best weight: 0.3834 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.124442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096494 restraints weight = 4246.957| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.32 r_work: 0.2877 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4385 Z= 0.120 Angle : 0.535 7.795 5979 Z= 0.275 Chirality : 0.041 0.185 666 Planarity : 0.004 0.031 722 Dihedral : 4.848 53.346 647 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.23 % Allowed : 21.88 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.37), residues: 525 helix: 1.64 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.90 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 257 TYR 0.018 0.001 TYR A 72 PHE 0.028 0.002 PHE A 398 TRP 0.012 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4381) covalent geometry : angle 0.52978 ( 5968) SS BOND : bond 0.00041 ( 1) SS BOND : angle 2.34749 ( 2) hydrogen bonds : bond 0.04754 ( 287) hydrogen bonds : angle 4.39815 ( 840) link_NAG-ASN : bond 0.00360 ( 3) link_NAG-ASN : angle 1.61967 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.104 Fit side-chains REVERT: A 163 GLN cc_start: 0.8241 (mt0) cc_final: 0.8030 (mt0) REVERT: A 172 ARG cc_start: 0.7592 (mtp180) cc_final: 0.7273 (mtp-110) REVERT: A 348 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 559 LEU cc_start: 0.7933 (mt) cc_final: 0.7554 (mt) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.5299 time to fit residues: 40.8257 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.121791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093381 restraints weight = 4285.459| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.35 r_work: 0.2831 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4385 Z= 0.138 Angle : 0.579 9.693 5979 Z= 0.297 Chirality : 0.043 0.185 666 Planarity : 0.004 0.032 722 Dihedral : 4.896 53.845 647 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.12 % Allowed : 20.76 % Favored : 76.12 % 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: 1.53 (0.37), residues: 525 helix: 1.66 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.92 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.023 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.013 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4381) covalent geometry : angle 0.57243 ( 5968) SS BOND : bond 0.00140 ( 1) SS BOND : angle 3.41285 ( 2) hydrogen bonds : bond 0.05392 ( 287) hydrogen bonds : angle 4.49801 ( 840) link_NAG-ASN : bond 0.00355 ( 3) link_NAG-ASN : angle 1.59505 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.174 Fit side-chains REVERT: A 348 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8265 (t) REVERT: A 485 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: A 559 LEU cc_start: 0.7979 (mt) cc_final: 0.7621 (mt) REVERT: A 572 GLN cc_start: 0.7534 (tp40) cc_final: 0.7079 (tt0) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.5519 time to fit residues: 41.2594 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.090551 restraints weight = 4264.909| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.36 r_work: 0.2778 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4385 Z= 0.172 Angle : 0.630 10.285 5979 Z= 0.326 Chirality : 0.045 0.188 666 Planarity : 0.004 0.034 722 Dihedral : 5.028 53.573 647 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 20.76 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.37), residues: 525 helix: 1.58 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.09 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 211 TYR 0.024 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.015 0.002 TRP A 116 HIS 0.001 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4381) covalent geometry : angle 0.62422 ( 5968) SS BOND : bond 0.00221 ( 1) SS BOND : angle 3.65269 ( 2) hydrogen bonds : bond 0.06226 ( 287) hydrogen bonds : angle 4.70035 ( 840) link_NAG-ASN : bond 0.00333 ( 3) link_NAG-ASN : angle 1.52541 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.179 Fit side-chains REVERT: A 485 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 559 LEU cc_start: 0.7969 (mt) cc_final: 0.7589 (mt) REVERT: A 572 GLN cc_start: 0.7512 (tp40) cc_final: 0.7051 (tt0) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.6299 time to fit residues: 50.0926 Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.090295 restraints weight = 4206.570| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.36 r_work: 0.2772 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4385 Z= 0.175 Angle : 0.633 11.025 5979 Z= 0.327 Chirality : 0.045 0.182 666 Planarity : 0.004 0.035 722 Dihedral : 5.052 53.870 647 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.57 % Allowed : 20.09 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.37), residues: 525 helix: 1.48 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.12 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.024 0.002 TYR A 72 PHE 0.031 0.002 PHE A 398 TRP 0.016 0.002 TRP A 116 HIS 0.001 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4381) covalent geometry : angle 0.62715 ( 5968) SS BOND : bond 0.00350 ( 1) SS BOND : angle 3.66736 ( 2) hydrogen bonds : bond 0.06264 ( 287) hydrogen bonds : angle 4.74284 ( 840) link_NAG-ASN : bond 0.00328 ( 3) link_NAG-ASN : angle 1.47891 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.154 Fit side-chains REVERT: A 57 CYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 559 LEU cc_start: 0.7978 (mt) cc_final: 0.7580 (mt) REVERT: A 572 GLN cc_start: 0.7511 (tp40) cc_final: 0.7050 (tt0) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.5389 time to fit residues: 41.4403 Evaluate side-chains 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092328 restraints weight = 4285.892| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.36 r_work: 0.2812 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4385 Z= 0.144 Angle : 0.598 11.745 5979 Z= 0.307 Chirality : 0.043 0.178 666 Planarity : 0.004 0.035 722 Dihedral : 4.919 54.447 647 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.46 % Allowed : 20.98 % Favored : 76.56 % 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: 1.35 (0.37), residues: 525 helix: 1.56 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.05 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.023 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4381) covalent geometry : angle 0.59395 ( 5968) SS BOND : bond 0.00317 ( 1) SS BOND : angle 2.87987 ( 2) hydrogen bonds : bond 0.05628 ( 287) hydrogen bonds : angle 4.61653 ( 840) link_NAG-ASN : bond 0.00318 ( 3) link_NAG-ASN : angle 1.44480 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.160 Fit side-chains REVERT: A 57 CYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8488 (m) REVERT: A 348 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8286 (t) REVERT: A 559 LEU cc_start: 0.8018 (mt) cc_final: 0.7624 (mt) REVERT: A 572 GLN cc_start: 0.7503 (tp40) cc_final: 0.7041 (tt0) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.5648 time to fit residues: 46.1815 Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.093445 restraints weight = 4224.123| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.34 r_work: 0.2827 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4385 Z= 0.137 Angle : 0.589 12.050 5979 Z= 0.301 Chirality : 0.042 0.174 666 Planarity : 0.004 0.033 722 Dihedral : 4.830 54.425 647 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.68 % Allowed : 20.76 % Favored : 76.56 % 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: 1.44 (0.37), residues: 525 helix: 1.61 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.99 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.022 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4381) covalent geometry : angle 0.58490 ( 5968) SS BOND : bond 0.00191 ( 1) SS BOND : angle 2.50505 ( 2) hydrogen bonds : bond 0.05429 ( 287) hydrogen bonds : angle 4.56425 ( 840) link_NAG-ASN : bond 0.00297 ( 3) link_NAG-ASN : angle 1.39560 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.185 Fit side-chains REVERT: A 57 CYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (m) REVERT: A 348 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (t) REVERT: A 559 LEU cc_start: 0.7945 (mt) cc_final: 0.7536 (mt) REVERT: A 572 GLN cc_start: 0.7540 (tp40) cc_final: 0.7084 (tt0) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.6056 time to fit residues: 50.7880 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.092751 restraints weight = 4251.101| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.36 r_work: 0.2822 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4385 Z= 0.142 Angle : 0.587 9.644 5979 Z= 0.303 Chirality : 0.043 0.183 666 Planarity : 0.004 0.034 722 Dihedral : 4.807 54.362 647 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.23 % Allowed : 21.21 % Favored : 76.56 % 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: 1.41 (0.37), residues: 525 helix: 1.60 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.02 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.023 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4381) covalent geometry : angle 0.58272 ( 5968) SS BOND : bond 0.00303 ( 1) SS BOND : angle 2.76800 ( 2) hydrogen bonds : bond 0.05569 ( 287) hydrogen bonds : angle 4.57589 ( 840) link_NAG-ASN : bond 0.00306 ( 3) link_NAG-ASN : angle 1.39638 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.39 seconds wall clock time: 32 minutes 8.41 seconds (1928.41 seconds total)