Starting phenix.real_space_refine on Fri May 9 23:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2e_38852/05_2025/8y2e_38852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2e_38852/05_2025/8y2e_38852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2e_38852/05_2025/8y2e_38852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2e_38852/05_2025/8y2e_38852.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2e_38852/05_2025/8y2e_38852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2e_38852/05_2025/8y2e_38852.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2813 2.51 5 N 659 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4214 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4163 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 504} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CXQ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.26, per 1000 atoms: 0.77 Number of scatterers: 4214 At special positions: 0 Unit cell: (74.8, 69.7, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 719 8.00 N 659 7.00 C 2813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 188 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 481.8 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.780A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.782A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.598A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.610A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.874A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.830A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.523A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.874A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.685A pdb=" N VAL A 382 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.521A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.111A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.544A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.293A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.593A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.898A pdb=" N TRP A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 268 hydrogen bonds defined for protein. 789 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1101 1.34 - 1.46: 925 1.46 - 1.58: 2282 1.58 - 1.70: 3 1.70 - 1.82: 34 Bond restraints: 4345 Sorted by residual: bond pdb=" C1 CXQ A 703 " pdb=" C5 CXQ A 703 " ideal model delta sigma weight residual 1.519 1.633 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C1 CXQ A 703 " pdb=" C4 CXQ A 703 " ideal model delta sigma weight residual 1.513 1.594 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C17 CXQ A 703 " pdb=" N1 CXQ A 703 " ideal model delta sigma weight residual 1.448 1.510 -0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" C1 CXQ A 703 " pdb=" O1 CXQ A 703 " ideal model delta sigma weight residual 1.397 1.458 -0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" N ILE A 268 " pdb=" CA ILE A 268 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.49e+00 ... (remaining 4340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5799 1.86 - 3.71: 114 3.71 - 5.57: 15 5.57 - 7.43: 2 7.43 - 9.28: 1 Bond angle restraints: 5931 Sorted by residual: angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 106.62 5.38 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" O ASP A 191 " ideal model delta sigma weight residual 120.92 117.41 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" CA PHE A 531 " pdb=" CB PHE A 531 " pdb=" CG PHE A 531 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CA ARG A 606 " pdb=" CB ARG A 606 " pdb=" CG ARG A 606 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 125.58 -9.28 3.50e+00 8.16e-02 7.04e+00 ... (remaining 5926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 2330 28.42 - 56.85: 151 56.85 - 85.27: 11 85.27 - 113.70: 0 113.70 - 142.12: 2 Dihedral angle restraints: 2494 sinusoidal: 973 harmonic: 1521 Sorted by residual: dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C8 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 158.12 16.00 142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C7 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 280.48 139.54 140.94 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA TRP A 132 " pdb=" C TRP A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 529 0.046 - 0.093: 116 0.093 - 0.139: 30 0.139 - 0.185: 2 0.185 - 0.231: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2 CXQ A 703 " pdb=" C13 CXQ A 703 " pdb=" C7 CXQ A 703 " pdb=" N1 CXQ A 703 " both_signs ideal model delta sigma weight residual False 2.74 2.92 -0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" C PRO A 584 " pdb=" CB PRO A 584 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 675 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 394 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.54e+00 pdb=" N PRO A 395 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 189 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C CYS A 189 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS A 189 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.016 2.00e-02 2.50e+03 1.47e-02 2.71e+00 pdb=" CG ASN A 181 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.015 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1154 2.81 - 3.33: 3834 3.33 - 3.85: 6643 3.85 - 4.38: 7416 4.38 - 4.90: 13745 Nonbonded interactions: 32792 Sorted by model distance: nonbonded pdb=" NH1 ARG A 237 " pdb=" OD1 ASN A 466 " model vdw 2.283 3.120 nonbonded pdb=" O ARG A 237 " pdb=" OG1 THR A 241 " model vdw 2.312 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OE2 GLU A 215 " model vdw 2.340 3.040 nonbonded pdb=" N ASP A 79 " pdb=" OD1 ASP A 79 " model vdw 2.409 3.120 nonbonded pdb=" O PHE A 498 " pdb=" NE2 GLN A 611 " model vdw 2.419 3.120 ... (remaining 32787 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: 2.050 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.005 0.114 4348 Z= 0.232 Angle : 0.614 9.283 5939 Z= 0.318 Chirality : 0.041 0.231 678 Planarity : 0.005 0.059 723 Dihedral : 17.534 142.121 1519 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 23.76 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.38), residues: 522 helix: 1.92 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 132 HIS 0.002 0.001 HIS A 225 PHE 0.016 0.001 PHE A 451 TYR 0.010 0.001 TYR A 575 ARG 0.001 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.01612 ( 2) link_NAG-ASN : angle 2.17487 ( 6) hydrogen bonds : bond 0.14037 ( 268) hydrogen bonds : angle 4.41491 ( 789) SS BOND : bond 0.00707 ( 1) SS BOND : angle 1.67162 ( 2) covalent geometry : bond 0.00485 ( 4345) covalent geometry : angle 0.60991 ( 5931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.449 Fit side-chains REVERT: A 126 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 531 PHE cc_start: 0.8123 (t80) cc_final: 0.7252 (t80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1642 time to fit residues: 10.2559 Evaluate side-chains 44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.132835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112347 restraints weight = 5082.736| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.77 r_work: 0.3091 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4348 Z= 0.129 Angle : 0.535 7.487 5939 Z= 0.269 Chirality : 0.037 0.122 678 Planarity : 0.004 0.060 723 Dihedral : 8.790 116.403 636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.71 % Allowed : 22.85 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.39), residues: 522 helix: 2.18 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.97 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.012 0.001 PHE A 412 TYR 0.013 0.001 TYR A 548 ARG 0.002 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 2) link_NAG-ASN : angle 1.31682 ( 6) hydrogen bonds : bond 0.05222 ( 268) hydrogen bonds : angle 3.98989 ( 789) SS BOND : bond 0.00497 ( 1) SS BOND : angle 1.56065 ( 2) covalent geometry : bond 0.00293 ( 4345) covalent geometry : angle 0.53308 ( 5931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.456 Fit side-chains REVERT: A 126 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 320 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6073 (t80) REVERT: A 424 MET cc_start: 0.6319 (mtp) cc_final: 0.5891 (mtt) REVERT: A 514 GLN cc_start: 0.7062 (tp40) cc_final: 0.6093 (pt0) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.1483 time to fit residues: 11.1953 Evaluate side-chains 54 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 517 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.130423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109979 restraints weight = 5096.917| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.77 r_work: 0.3061 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4348 Z= 0.134 Angle : 0.516 6.356 5939 Z= 0.260 Chirality : 0.038 0.118 678 Planarity : 0.005 0.062 723 Dihedral : 7.886 105.069 636 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.52 % Allowed : 21.27 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.38), residues: 522 helix: 2.07 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 477 PHE 0.016 0.001 PHE A 451 TYR 0.010 0.001 TYR A 548 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 2) link_NAG-ASN : angle 1.05094 ( 6) hydrogen bonds : bond 0.05443 ( 268) hydrogen bonds : angle 3.97903 ( 789) SS BOND : bond 0.00469 ( 1) SS BOND : angle 1.24386 ( 2) covalent geometry : bond 0.00312 ( 4345) covalent geometry : angle 0.51489 ( 5931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.431 Fit side-chains REVERT: A 320 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.5845 (t80) REVERT: A 514 GLN cc_start: 0.7035 (tp40) cc_final: 0.5873 (pt0) outliers start: 20 outliers final: 14 residues processed: 59 average time/residue: 0.1579 time to fit residues: 12.1920 Evaluate side-chains 58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.130017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109856 restraints weight = 5100.663| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.74 r_work: 0.3069 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4348 Z= 0.129 Angle : 0.506 6.220 5939 Z= 0.256 Chirality : 0.037 0.113 678 Planarity : 0.004 0.061 723 Dihedral : 7.380 96.658 636 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.07 % Allowed : 22.40 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.38), residues: 522 helix: 2.07 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.30 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.015 0.001 PHE A 451 TYR 0.010 0.001 TYR A 548 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 2) link_NAG-ASN : angle 1.03787 ( 6) hydrogen bonds : bond 0.05207 ( 268) hydrogen bonds : angle 3.99056 ( 789) SS BOND : bond 0.00436 ( 1) SS BOND : angle 1.22872 ( 2) covalent geometry : bond 0.00300 ( 4345) covalent geometry : angle 0.50475 ( 5931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.461 Fit side-chains REVERT: A 156 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8061 (t80) REVERT: A 320 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.5835 (t80) REVERT: A 514 GLN cc_start: 0.7025 (tp40) cc_final: 0.5813 (pt0) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.1464 time to fit residues: 11.0264 Evaluate side-chains 58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 11 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 overall best weight: 0.3968 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.133720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113442 restraints weight = 5109.223| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.76 r_work: 0.3115 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4348 Z= 0.100 Angle : 0.459 6.058 5939 Z= 0.233 Chirality : 0.036 0.115 678 Planarity : 0.004 0.057 723 Dihedral : 6.942 89.598 636 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.52 % Allowed : 21.95 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.39), residues: 522 helix: 2.14 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.24 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.001 0.000 HIS A 179 PHE 0.015 0.001 PHE A 451 TYR 0.006 0.001 TYR A 575 ARG 0.003 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 2) link_NAG-ASN : angle 0.93427 ( 6) hydrogen bonds : bond 0.04105 ( 268) hydrogen bonds : angle 3.87125 ( 789) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.95416 ( 2) covalent geometry : bond 0.00215 ( 4345) covalent geometry : angle 0.45793 ( 5931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.420 Fit side-chains REVERT: A 156 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7940 (t80) REVERT: A 320 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.5794 (t80) REVERT: A 416 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7484 (tp) outliers start: 20 outliers final: 12 residues processed: 56 average time/residue: 0.1270 time to fit residues: 9.7320 Evaluate side-chains 54 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.134405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115333 restraints weight = 5023.995| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.58 r_work: 0.3115 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4348 Z= 0.116 Angle : 0.484 6.167 5939 Z= 0.244 Chirality : 0.037 0.113 678 Planarity : 0.004 0.060 723 Dihedral : 6.813 87.106 636 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.85 % Allowed : 22.17 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.38), residues: 522 helix: 2.04 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.23 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.015 0.001 PHE A 451 TYR 0.009 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 2) link_NAG-ASN : angle 0.92819 ( 6) hydrogen bonds : bond 0.04701 ( 268) hydrogen bonds : angle 3.92902 ( 789) SS BOND : bond 0.00352 ( 1) SS BOND : angle 1.03723 ( 2) covalent geometry : bond 0.00263 ( 4345) covalent geometry : angle 0.48274 ( 5931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.407 Fit side-chains REVERT: A 156 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 320 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.6055 (t80) REVERT: A 416 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7688 (tp) REVERT: A 514 GLN cc_start: 0.7035 (tp40) cc_final: 0.5898 (pt0) outliers start: 17 outliers final: 12 residues processed: 56 average time/residue: 0.1449 time to fit residues: 10.7098 Evaluate side-chains 57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.131011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110723 restraints weight = 5077.853| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.75 r_work: 0.3091 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4348 Z= 0.119 Angle : 0.489 6.606 5939 Z= 0.248 Chirality : 0.037 0.113 678 Planarity : 0.004 0.060 723 Dihedral : 6.732 84.883 636 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.30 % Allowed : 21.95 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.38), residues: 522 helix: 2.08 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.31 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 PHE 0.016 0.001 PHE A 451 TYR 0.011 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 2) link_NAG-ASN : angle 0.91518 ( 6) hydrogen bonds : bond 0.04802 ( 268) hydrogen bonds : angle 3.95144 ( 789) SS BOND : bond 0.00363 ( 1) SS BOND : angle 1.07861 ( 2) covalent geometry : bond 0.00271 ( 4345) covalent geometry : angle 0.48851 ( 5931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.410 Fit side-chains REVERT: A 156 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 320 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.5854 (t80) REVERT: A 416 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7535 (tp) REVERT: A 514 GLN cc_start: 0.6968 (tp40) cc_final: 0.5712 (pt0) outliers start: 19 outliers final: 14 residues processed: 56 average time/residue: 0.1275 time to fit residues: 9.7514 Evaluate side-chains 57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.0010 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.133819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.113566 restraints weight = 4979.528| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.75 r_work: 0.3125 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4348 Z= 0.099 Angle : 0.458 6.726 5939 Z= 0.231 Chirality : 0.036 0.113 678 Planarity : 0.004 0.057 723 Dihedral : 6.461 80.320 636 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.85 % Allowed : 22.40 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 522 helix: 2.21 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.23 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.001 0.000 HIS A 179 PHE 0.016 0.001 PHE A 451 TYR 0.007 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 2) link_NAG-ASN : angle 0.85308 ( 6) hydrogen bonds : bond 0.03988 ( 268) hydrogen bonds : angle 3.85890 ( 789) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.97973 ( 2) covalent geometry : bond 0.00212 ( 4345) covalent geometry : angle 0.45703 ( 5931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.416 Fit side-chains REVERT: A 156 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7950 (t80) REVERT: A 320 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.5798 (t80) REVERT: A 416 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7458 (tp) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.1454 time to fit residues: 10.5800 Evaluate side-chains 56 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.130324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109995 restraints weight = 5088.891| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.75 r_work: 0.3067 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4348 Z= 0.130 Angle : 0.506 7.343 5939 Z= 0.255 Chirality : 0.038 0.115 678 Planarity : 0.004 0.060 723 Dihedral : 6.509 80.050 636 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.07 % Allowed : 22.17 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.38), residues: 522 helix: 2.19 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.40 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 477 PHE 0.016 0.001 PHE A 451 TYR 0.011 0.001 TYR A 575 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 2) link_NAG-ASN : angle 0.97654 ( 6) hydrogen bonds : bond 0.05028 ( 268) hydrogen bonds : angle 3.96698 ( 789) SS BOND : bond 0.00379 ( 1) SS BOND : angle 1.09405 ( 2) covalent geometry : bond 0.00302 ( 4345) covalent geometry : angle 0.50462 ( 5931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.434 Fit side-chains REVERT: A 156 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 320 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.5883 (t80) REVERT: A 416 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7559 (tp) REVERT: A 514 GLN cc_start: 0.6984 (tp40) cc_final: 0.5693 (pt0) outliers start: 18 outliers final: 15 residues processed: 57 average time/residue: 0.1502 time to fit residues: 11.3252 Evaluate side-chains 60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.0770 chunk 7 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.131953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111737 restraints weight = 5021.288| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.74 r_work: 0.3089 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4348 Z= 0.108 Angle : 0.482 7.662 5939 Z= 0.243 Chirality : 0.037 0.113 678 Planarity : 0.004 0.058 723 Dihedral : 6.398 78.095 636 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.30 % Allowed : 21.95 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.38), residues: 522 helix: 2.24 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.36 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.002 0.001 HIS A 179 PHE 0.016 0.001 PHE A 451 TYR 0.008 0.001 TYR A 575 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 2) link_NAG-ASN : angle 0.91692 ( 6) hydrogen bonds : bond 0.04434 ( 268) hydrogen bonds : angle 3.90742 ( 789) SS BOND : bond 0.00328 ( 1) SS BOND : angle 1.02500 ( 2) covalent geometry : bond 0.00238 ( 4345) covalent geometry : angle 0.48089 ( 5931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.437 Fit side-chains REVERT: A 156 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8014 (t80) REVERT: A 320 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.5850 (t80) REVERT: A 416 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7512 (tp) REVERT: A 514 GLN cc_start: 0.7000 (tp40) cc_final: 0.5646 (pt0) outliers start: 19 outliers final: 15 residues processed: 58 average time/residue: 0.1478 time to fit residues: 11.3034 Evaluate side-chains 61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.129672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.109309 restraints weight = 5074.411| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.75 r_work: 0.3065 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4348 Z= 0.132 Angle : 0.515 7.863 5939 Z= 0.260 Chirality : 0.038 0.116 678 Planarity : 0.004 0.061 723 Dihedral : 6.443 77.815 636 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.07 % Allowed : 22.17 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.38), residues: 522 helix: 2.15 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.42 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.002 0.001 HIS A 477 PHE 0.016 0.001 PHE A 451 TYR 0.011 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 2) link_NAG-ASN : angle 1.01324 ( 6) hydrogen bonds : bond 0.05161 ( 268) hydrogen bonds : angle 3.98818 ( 789) SS BOND : bond 0.00380 ( 1) SS BOND : angle 1.10620 ( 2) covalent geometry : bond 0.00309 ( 4345) covalent geometry : angle 0.51395 ( 5931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.39 seconds wall clock time: 41 minutes 28.07 seconds (2488.07 seconds total)