Starting phenix.real_space_refine on Thu Sep 10 22:07:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7y_33674/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7y_33674/09_2026/7y7y_33674.cif" } 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-2.2.1-6174/lib/python3.11/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 chiralities: 3 Time building chain proxies: 0.97, per 1000 atoms: 0.23 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: 0.32 Conformation dependent library (CDL) restraints added in 153.1 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: 0.10 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: 0.55 Time building geometry restraints manager: 0.45 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: 2089 17.05 - 34.11: 266 34.11 - 51.16: 75 51.16 - 68.22: 19 68.22 - 85.27: 6 Dihedral angle restraints: 2455 sinusoidal: 936 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 2452 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.140 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 17.116 85.271 1488 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/Z covalent geometry : bond 0.00541 / 0.26 ( 4381) covalent geometry : angle 0.72532 / 0.40 ( 5968) SS BOND : bond 0.02058 / 1.08 ( 1) SS BOND : angle 6.40781 / 3.57 ( 2) hydrogen bonds : bond 0.13720 / 9.26 ( 287) hydrogen bonds : angle 6.19573 / 4.44 ( 840) link_NAG-ASN : bond 0.16995 / 8.83 ( 3) link_NAG-ASN : angle 7.70618 / 4.54 ( 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 : 0.127 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: 0.5455 time to fit residues: 36.6882 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 : 0.166 ------------------------------------------------------------------------------- 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... ** 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 = 0.3324 r_free = 0.3324 target = 0.119640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.091543 restraints weight = 4224.343| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.36 r_work: 0.2795 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4385 Z= 0.153 Angle : 0.615 7.847 5979 Z= 0.322 Chirality : 0.044 0.229 666 Planarity : 0.004 0.034 722 Dihedral : 5.278 50.849 587 Min Nonbonded Distance : 2.185 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: 0.99 (0.37), residues: 525 helix: 1.27 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.023 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/Z covalent geometry : bond 0.00335 / 0.15 ( 4381) covalent geometry : angle 0.60209 / 0.32 ( 5968) SS BOND : bond 0.00289 / 0.15 ( 1) SS BOND : angle 1.56315 / 0.88 ( 2) hydrogen bonds : bond 0.06042 / 4.05 ( 287) hydrogen bonds : angle 4.82342 / 3.50 ( 840) link_NAG-ASN : bond 0.00513 / 0.26 ( 3) link_NAG-ASN : angle 3.21064 / 1.89 ( 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: 0.8590 (mt0) cc_final: 0.8322 (mt0) REVERT: A 485 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: A 559 LEU cc_start: 0.7631 (mt) cc_final: 0.7333 (mt) REVERT: A 572 GLN cc_start: 0.7477 (tp40) cc_final: 0.7030 (tt0) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.4826 time to fit residues: 35.1607 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 : 0.130 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3317 r_free = 0.3317 target = 0.119059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090548 restraints weight = 4193.334| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.37 r_work: 0.2776 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4385 Z= 0.169 Angle : 0.629 8.110 5979 Z= 0.329 Chirality : 0.045 0.227 666 Planarity : 0.004 0.036 722 Dihedral : 5.224 52.218 584 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.12 % Allowed : 21.65 % 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: 1.11 (0.37), residues: 525 helix: 1.39 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.09 (0.54), residues: 137 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 0.030 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/Z covalent geometry : bond 0.00389 / 0.17 ( 4381) covalent geometry : angle 0.61713 / 0.32 ( 5968) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 4.71234 / 2.50 ( 2) hydrogen bonds : bond 0.06287 / 4.21 ( 287) hydrogen bonds : angle 4.81621 / 3.51 ( 840) link_NAG-ASN : bond 0.00415 / 0.20 ( 3) link_NAG-ASN : angle 2.32965 / 1.42 ( 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 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.127 Fit side-chains REVERT: A 163 GLN cc_start: 0.8350 (mt0) cc_final: 0.8079 (mt0) REVERT: A 485 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: A 559 LEU cc_start: 0.7727 (mt) cc_final: 0.7499 (mt) REVERT: A 572 GLN cc_start: 0.7479 (tp40) cc_final: 0.7047 (tt0) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.4542 time to fit residues: 33.5948 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 : 0.132 ------------------------------------------------------------------------------- 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: 0.1980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.093519 restraints weight = 4177.508| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.34 r_work: 0.2828 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4385 Z= 0.134 Angle : 0.571 8.346 5979 Z= 0.296 Chirality : 0.042 0.197 666 Planarity : 0.004 0.033 722 Dihedral : 5.008 53.009 584 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 22.10 % Favored : 75.00 % 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: 1.33 (0.37), residues: 525 helix: 1.55 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.10 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.021 0.001 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/Z covalent geometry : bond 0.00292 / 0.13 ( 4381) covalent geometry : angle 0.56199 / 0.29 ( 5968) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 3.67765 / 1.94 ( 2) hydrogen bonds : bond 0.05377 / 3.60 ( 287) hydrogen bonds : angle 4.60533 / 3.35 ( 840) link_NAG-ASN : bond 0.00371 / 0.18 ( 3) link_NAG-ASN : angle 2.09857 / 1.25 ( 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 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.100 Fit side-chains REVERT: A 163 GLN cc_start: 0.8283 (mt0) cc_final: 0.8041 (mt0) REVERT: A 348 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 559 LEU cc_start: 0.7866 (mt) cc_final: 0.7493 (mt) REVERT: A 572 GLN cc_start: 0.7470 (tp40) cc_final: 0.7018 (tt0) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.4931 time to fit residues: 36.8427 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 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 = 0.3348 r_free = 0.3348 target = 0.121378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.092879 restraints weight = 4220.577| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.35 r_work: 0.2820 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1527 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= 0.139 Angle : 0.572 9.162 5979 Z= 0.296 Chirality : 0.043 0.182 666 Planarity : 0.004 0.032 722 Dihedral : 4.999 53.496 584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.68 % Allowed : 21.43 % 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: 1.36 (0.37), residues: 525 helix: 1.58 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.09 (0.54), 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 0.013 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4381) covalent geometry : angle 0.56631 / 0.29 ( 5968) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 3.13462 / 1.66 ( 2) hydrogen bonds : bond 0.05505 / 3.69 ( 287) hydrogen bonds : angle 4.59396 / 3.34 ( 840) link_NAG-ASN : bond 0.00346 / 0.17 ( 3) link_NAG-ASN : angle 1.65754 / 1.02 ( 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 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.168 Fit side-chains REVERT: A 163 GLN cc_start: 0.8285 (mt0) cc_final: 0.8082 (mt0) REVERT: A 172 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7340 (mtp-110) REVERT: A 348 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8297 (t) REVERT: A 485 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: A 559 LEU cc_start: 0.7948 (mt) cc_final: 0.7568 (mt) REVERT: A 572 GLN cc_start: 0.7499 (tp40) cc_final: 0.7045 (tt0) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.4958 time to fit residues: 38.1694 Evaluate side-chains 72 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.121281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093032 restraints weight = 4312.963| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.35 r_work: 0.2823 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4385 Z= 0.140 Angle : 0.577 9.678 5979 Z= 0.297 Chirality : 0.043 0.179 666 Planarity : 0.004 0.033 722 Dihedral : 4.982 53.666 584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.72 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: 1.40 (0.37), residues: 525 helix: 1.58 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 132 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/Z covalent geometry : bond 0.00311 / 0.14 ( 4381) covalent geometry : angle 0.57195 / 0.30 ( 5968) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 2.99450 / 1.58 ( 2) hydrogen bonds : bond 0.05491 / 3.68 ( 287) hydrogen bonds : angle 4.58066 / 3.33 ( 840) link_NAG-ASN : bond 0.00336 / 0.16 ( 3) link_NAG-ASN : angle 1.58394 / 1.00 ( 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 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.114 Fit side-chains REVERT: A 163 GLN cc_start: 0.8328 (mt0) cc_final: 0.8119 (mt0) REVERT: A 172 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7224 (mtp-110) REVERT: A 348 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8216 (t) REVERT: A 485 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: A 559 LEU cc_start: 0.7885 (mt) cc_final: 0.7499 (mt) REVERT: A 572 GLN cc_start: 0.7475 (tp40) cc_final: 0.7012 (tt0) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.4819 time to fit residues: 36.5740 Evaluate side-chains 82 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 11 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.7344 > 50:) chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.121311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093003 restraints weight = 4297.171| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.35 r_work: 0.2821 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1610 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= 0.140 Angle : 0.578 10.370 5979 Z= 0.296 Chirality : 0.043 0.178 666 Planarity : 0.004 0.033 722 Dihedral : 4.984 54.047 584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 20.31 % Favored : 76.79 % 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: 1.43 (0.37), residues: 525 helix: 1.60 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.99 (0.54), residues: 132 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/Z covalent geometry : bond 0.00311 / 0.14 ( 4381) covalent geometry : angle 0.57278 / 0.29 ( 5968) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 2.91121 / 1.54 ( 2) hydrogen bonds : bond 0.05471 / 3.67 ( 287) hydrogen bonds : angle 4.57242 / 3.32 ( 840) link_NAG-ASN : bond 0.00317 / 0.15 ( 3) link_NAG-ASN : angle 1.49193 / 0.95 ( 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 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.118 Fit side-chains REVERT: A 172 ARG cc_start: 0.7482 (mtp180) cc_final: 0.7227 (mtp-110) REVERT: A 348 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8262 (t) REVERT: A 485 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: A 559 LEU cc_start: 0.7983 (mt) cc_final: 0.7623 (mt) REVERT: A 572 GLN cc_start: 0.7510 (tp40) cc_final: 0.7047 (tt0) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.5603 time to fit residues: 45.7850 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 : 0.160 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.090194 restraints weight = 4214.545| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.36 r_work: 0.2771 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4385 Z= 0.176 Angle : 0.635 11.606 5979 Z= 0.327 Chirality : 0.046 0.185 666 Planarity : 0.004 0.035 722 Dihedral : 5.182 53.567 584 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 20.31 % Favored : 76.79 % 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: 525 helix: 1.51 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.14 (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 0.015 0.002 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 4381) covalent geometry : angle 0.62995 / 0.33 ( 5968) SS BOND : bond 0.00167 / 0.09 ( 1) SS BOND : angle 3.69579 / 1.95 ( 2) hydrogen bonds : bond 0.06329 / 4.25 ( 287) hydrogen bonds : angle 4.76574 / 3.47 ( 840) link_NAG-ASN : bond 0.00311 / 0.15 ( 3) link_NAG-ASN : angle 1.43028 / 0.90 ( 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 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.171 Fit side-chains REVERT: A 57 CYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8473 (m) REVERT: A 172 ARG cc_start: 0.7313 (mtp180) cc_final: 0.7088 (mtp-110) REVERT: A 485 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: A 559 LEU cc_start: 0.7916 (mt) cc_final: 0.7565 (mt) REVERT: A 572 GLN cc_start: 0.7502 (tp40) cc_final: 0.7043 (tt0) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.5179 time to fit residues: 40.9591 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.121544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.093215 restraints weight = 4304.894| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.35 r_work: 0.2830 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1645 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= 0.135 Angle : 0.578 11.345 5979 Z= 0.296 Chirality : 0.042 0.173 666 Planarity : 0.004 0.034 722 Dihedral : 5.014 54.334 584 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 20.31 % Favored : 76.79 % 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: 1.42 (0.37), residues: 525 helix: 1.58 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.96 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 417 TYR 0.022 0.001 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/Z covalent geometry : bond 0.00296 / 0.14 ( 4381) covalent geometry : angle 0.57367 / 0.29 ( 5968) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 2.85266 / 1.51 ( 2) hydrogen bonds : bond 0.05374 / 3.59 ( 287) hydrogen bonds : angle 4.57779 / 3.33 ( 840) link_NAG-ASN : bond 0.00316 / 0.15 ( 3) link_NAG-ASN : angle 1.36161 / 0.84 ( 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 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.160 Fit side-chains REVERT: A 57 CYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8465 (m) REVERT: A 348 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 485 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 559 LEU cc_start: 0.7995 (mt) cc_final: 0.7600 (mt) REVERT: A 572 GLN cc_start: 0.7505 (tp40) cc_final: 0.7044 (tt0) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.5577 time to fit residues: 45.7128 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.093215 restraints weight = 4231.791| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.34 r_work: 0.2827 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1678 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= 0.138 Angle : 0.584 11.469 5979 Z= 0.300 Chirality : 0.042 0.167 666 Planarity : 0.004 0.033 722 Dihedral : 4.999 54.496 584 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.90 % Allowed : 20.31 % Favored : 76.79 % 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: 1.62 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -1.02 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 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/Z covalent geometry : bond 0.00306 / 0.14 ( 4381) covalent geometry : angle 0.58063 / 0.30 ( 5968) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 2.68322 / 1.42 ( 2) hydrogen bonds : bond 0.05461 / 3.64 ( 287) hydrogen bonds : angle 4.57504 / 3.33 ( 840) link_NAG-ASN : bond 0.00301 / 0.14 ( 3) link_NAG-ASN : angle 1.28495 / 0.81 ( 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 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.158 Fit side-chains REVERT: A 54 LEU cc_start: 0.8971 (tp) cc_final: 0.8615 (tm) REVERT: A 57 CYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (m) REVERT: A 172 ARG cc_start: 0.7511 (mtp-110) cc_final: 0.7276 (mtp180) REVERT: A 348 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8253 (t) REVERT: A 485 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: A 559 LEU cc_start: 0.7845 (mt) cc_final: 0.7471 (mt) REVERT: A 572 GLN cc_start: 0.7557 (tp40) cc_final: 0.7105 (tt0) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.4577 time to fit residues: 34.3056 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 164 CYS 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 485 GLN 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: 0.5980 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.092893 restraints weight = 4273.622| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.35 r_work: 0.2827 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1670 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= 0.140 Angle : 0.582 9.541 5979 Z= 0.300 Chirality : 0.043 0.183 666 Planarity : 0.004 0.034 722 Dihedral : 4.991 54.487 584 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 20.54 % 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: 1.42 (0.37), residues: 525 helix: 1.60 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -1.02 (0.54), residues: 132 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/Z covalent geometry : bond 0.00313 / 0.14 ( 4381) covalent geometry : angle 0.57793 / 0.30 ( 5968) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 2.88082 / 1.53 ( 2) hydrogen bonds : bond 0.05502 / 3.68 ( 287) hydrogen bonds : angle 4.56992 / 3.33 ( 840) link_NAG-ASN : bond 0.00312 / 0.15 ( 3) link_NAG-ASN : angle 1.28528 / 0.79 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.83 seconds wall clock time: 29 minutes 19.76 seconds (1759.76 seconds total)