Starting phenix.real_space_refine on Wed Jul 23 23:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdg_61392/07_2025/9jdg_61392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdg_61392/07_2025/9jdg_61392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2025/9jdg_61392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2025/9jdg_61392.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2025/9jdg_61392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdg_61392/07_2025/9jdg_61392_neut.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3021 2.51 5 N 655 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4459 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4311 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 148 Unusual residues: {' CL': 1, 'D10': 5, 'D12': 3, 'NAG': 1, 'OCT': 5} Classifications: {'undetermined': 15, 'water': 7} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.29, per 1000 atoms: 0.74 Number of scatterers: 4459 At special positions: 0 Unit cell: (87.565, 67.52, 88.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 750 8.00 N 655 7.00 C 3021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 715 " - " ASN A 190 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 496.7 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 77.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.616A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.080A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.238A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.347A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.595A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.563A pdb=" N VAL A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 266 removed outlier: 4.046A pdb=" N THR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.708A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.522A pdb=" N ILE A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.551A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.798A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.641A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.568A pdb=" N GLY A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 449 No H-bonds generated for 'chain 'A' and resid 448 through 449' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.043A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.563A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.960A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 274 hydrogen bonds defined for protein. 816 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: 1.16 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1257 1.34 - 1.46: 957 1.46 - 1.57: 2319 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4579 Sorted by residual: bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.46e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.21e+00 bond pdb=" N PHE A 191 " pdb=" CA PHE A 191 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.17e+00 bond pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 ... (remaining 4574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 5956 1.52 - 3.04: 207 3.04 - 4.56: 25 4.56 - 6.08: 6 6.08 - 7.59: 3 Bond angle restraints: 6197 Sorted by residual: angle pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" O GLY A 594 " ideal model delta sigma weight residual 121.58 118.17 3.41 9.00e-01 1.23e+00 1.44e+01 angle pdb=" CA ARG A 587 " pdb=" C ARG A 587 " pdb=" O ARG A 587 " ideal model delta sigma weight residual 122.63 118.06 4.57 1.29e+00 6.01e-01 1.26e+01 angle pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" O VAL A 203 " ideal model delta sigma weight residual 121.05 117.51 3.54 1.11e+00 8.12e-01 1.02e+01 angle pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" O SER A 205 " ideal model delta sigma weight residual 122.14 118.31 3.83 1.24e+00 6.50e-01 9.53e+00 angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 111.24 106.99 4.25 1.38e+00 5.25e-01 9.48e+00 ... (remaining 6192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 2328 16.12 - 32.24: 222 32.24 - 48.36: 55 48.36 - 64.48: 10 64.48 - 80.60: 4 Dihedral angle restraints: 2619 sinusoidal: 1051 harmonic: 1568 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TRP A 166 " pdb=" C TRP A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CB MET A 452 " pdb=" CG MET A 452 " pdb=" SD MET A 452 " pdb=" CE MET A 452 " ideal model delta sinusoidal sigma weight residual -180.00 -125.19 -54.81 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 2616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 662 0.112 - 0.224: 14 0.224 - 0.336: 0 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 677 Sorted by residual: chirality pdb=" C1 NAG A 715 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 715 " pdb=" O5 NAG A 715 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA ILE A 196 " pdb=" N ILE A 196 " pdb=" C ILE A 196 " pdb=" CB ILE A 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 674 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.161 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" CG ASN A 190 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.335 2.00e-02 2.50e+03 pdb=" C1 NAG A 715 " -0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 715 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG A 715 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 715 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 715 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A 715 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 587 " -0.158 9.50e-02 1.11e+02 7.10e-02 3.10e+00 pdb=" NE ARG A 587 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 587 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 587 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 587 " -0.005 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 60 2.67 - 3.23: 4352 3.23 - 3.78: 6909 3.78 - 4.34: 9759 4.34 - 4.90: 16317 Nonbonded interactions: 37397 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.109 3.040 nonbonded pdb=" ND2 ASN A 190 " pdb=" N2 NAG A 715 " model vdw 2.113 2.560 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.275 3.120 nonbonded pdb=" NE2 GLN A 289 " pdb=" OD1 ASP A 293 " model vdw 2.280 3.120 nonbonded pdb=" O ALA A 433 " pdb=" OG SER A 437 " model vdw 2.356 3.040 ... (remaining 37392 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: 0.010 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.600 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.006 0.177 4581 Z= 0.316 Angle : 0.839 33.872 6202 Z= 0.431 Chirality : 0.047 0.560 677 Planarity : 0.006 0.071 745 Dihedral : 13.695 80.598 1624 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.22 % Allowed : 0.43 % Favored : 99.35 % 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: -0.46 (0.35), residues: 541 helix: 0.21 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 161 PHE 0.017 0.001 PHE A 95 TYR 0.019 0.001 TYR A 578 ARG 0.004 0.000 ARG A 564 Details of bonding type rmsd link_NAG-ASN : bond 0.17731 ( 1) link_NAG-ASN : angle 23.72417 ( 3) hydrogen bonds : bond 0.23369 ( 274) hydrogen bonds : angle 7.71198 ( 816) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.97443 ( 2) covalent geometry : bond 0.00534 ( 4579) covalent geometry : angle 0.65574 ( 6197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7703 (mmp) cc_final: 0.7380 (mmp) REVERT: A 427 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6096 (mtm180) REVERT: A 460 TYR cc_start: 0.8990 (t80) cc_final: 0.8752 (t80) REVERT: A 566 CYS cc_start: 0.8157 (m) cc_final: 0.7941 (m) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1526 time to fit residues: 11.5449 Evaluate side-chains 49 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.093943 restraints weight = 5475.646| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.75 r_work: 0.2814 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4581 Z= 0.140 Angle : 0.542 7.522 6202 Z= 0.281 Chirality : 0.039 0.124 677 Planarity : 0.004 0.038 745 Dihedral : 5.945 42.969 698 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.87 % Allowed : 6.96 % Favored : 92.17 % 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: 0.53 (0.35), residues: 541 helix: 1.03 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.25 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.014 0.001 PHE A 338 TYR 0.015 0.001 TYR A 69 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 0.96954 ( 3) hydrogen bonds : bond 0.05008 ( 274) hydrogen bonds : angle 4.87729 ( 816) SS BOND : bond 0.00132 ( 1) SS BOND : angle 1.50254 ( 2) covalent geometry : bond 0.00310 ( 4579) covalent geometry : angle 0.54129 ( 6197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.446 Fit side-chains REVERT: A 351 MET cc_start: 0.8597 (mtp) cc_final: 0.8320 (mtm) REVERT: A 406 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8263 (mm-30) REVERT: A 427 ARG cc_start: 0.6935 (mtm180) cc_final: 0.6194 (mtm180) outliers start: 4 outliers final: 1 residues processed: 63 average time/residue: 0.1300 time to fit residues: 11.1642 Evaluate side-chains 54 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.119050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.092861 restraints weight = 5556.309| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.68 r_work: 0.2796 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4581 Z= 0.166 Angle : 0.542 7.149 6202 Z= 0.275 Chirality : 0.040 0.128 677 Planarity : 0.004 0.035 745 Dihedral : 5.870 33.755 698 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.52 % Allowed : 9.13 % Favored : 89.35 % 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: 0.72 (0.35), residues: 541 helix: 1.19 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 PHE 0.015 0.001 PHE A 474 TYR 0.032 0.001 TYR A 460 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.07606 ( 3) hydrogen bonds : bond 0.04492 ( 274) hydrogen bonds : angle 4.62853 ( 816) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.55771 ( 2) covalent geometry : bond 0.00396 ( 4579) covalent geometry : angle 0.54108 ( 6197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.457 Fit side-chains REVERT: A 309 MET cc_start: 0.7884 (mmp) cc_final: 0.7468 (mmp) REVERT: A 427 ARG cc_start: 0.6881 (mtm180) cc_final: 0.6192 (mtm180) REVERT: A 577 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7869 (tppt) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1474 time to fit residues: 11.4853 Evaluate side-chains 57 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.094255 restraints weight = 5584.826| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.67 r_work: 0.2818 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4581 Z= 0.135 Angle : 0.507 7.082 6202 Z= 0.256 Chirality : 0.039 0.121 677 Planarity : 0.004 0.033 745 Dihedral : 5.602 34.998 698 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.39 % Allowed : 9.78 % Favored : 87.83 % 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: 0.96 (0.35), residues: 541 helix: 1.43 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS A 161 PHE 0.012 0.001 PHE A 474 TYR 0.022 0.001 TYR A 460 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 0.89175 ( 3) hydrogen bonds : bond 0.04049 ( 274) hydrogen bonds : angle 4.43768 ( 816) SS BOND : bond 0.00090 ( 1) SS BOND : angle 1.19517 ( 2) covalent geometry : bond 0.00317 ( 4579) covalent geometry : angle 0.50593 ( 6197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.455 Fit side-chains REVERT: A 172 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7265 (ttm) REVERT: A 176 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8177 (mtp) REVERT: A 309 MET cc_start: 0.7904 (mmp) cc_final: 0.7413 (mmp) REVERT: A 321 ASN cc_start: 0.8205 (t0) cc_final: 0.7772 (t0) REVERT: A 351 MET cc_start: 0.8719 (mtp) cc_final: 0.8399 (mtm) REVERT: A 427 ARG cc_start: 0.6944 (mtm180) cc_final: 0.6241 (mtm180) REVERT: A 577 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7858 (tppt) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 0.1429 time to fit residues: 12.0961 Evaluate side-chains 59 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 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 = 0.3267 r_free = 0.3267 target = 0.120026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.093748 restraints weight = 5714.714| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.71 r_work: 0.2829 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4581 Z= 0.144 Angle : 0.512 7.046 6202 Z= 0.258 Chirality : 0.039 0.123 677 Planarity : 0.004 0.033 745 Dihedral : 5.600 36.942 698 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.17 % Allowed : 11.09 % Favored : 86.74 % 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: 1.05 (0.35), residues: 541 helix: 1.53 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 PHE 0.013 0.001 PHE A 474 TYR 0.019 0.001 TYR A 69 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00011 ( 1) link_NAG-ASN : angle 0.84777 ( 3) hydrogen bonds : bond 0.04009 ( 274) hydrogen bonds : angle 4.41107 ( 816) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.79767 ( 2) covalent geometry : bond 0.00343 ( 4579) covalent geometry : angle 0.51113 ( 6197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.493 Fit side-chains REVERT: A 172 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7249 (ttm) REVERT: A 176 MET cc_start: 0.8682 (mtp) cc_final: 0.8234 (mtp) REVERT: A 292 ILE cc_start: 0.8341 (mm) cc_final: 0.8130 (mt) REVERT: A 309 MET cc_start: 0.7951 (mmp) cc_final: 0.7460 (mmp) REVERT: A 321 ASN cc_start: 0.8239 (t0) cc_final: 0.7800 (t0) REVERT: A 427 ARG cc_start: 0.7005 (mtm180) cc_final: 0.6307 (mtm180) REVERT: A 452 MET cc_start: 0.8974 (tpt) cc_final: 0.8693 (tpt) REVERT: A 577 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7745 (tppt) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.1642 time to fit residues: 13.1696 Evaluate side-chains 59 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.122832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095209 restraints weight = 5533.561| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.84 r_work: 0.2851 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4581 Z= 0.115 Angle : 0.485 7.002 6202 Z= 0.244 Chirality : 0.038 0.129 677 Planarity : 0.004 0.032 745 Dihedral : 5.309 38.184 698 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.52 % Allowed : 12.61 % Favored : 85.87 % 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: 1.31 (0.36), residues: 541 helix: 1.76 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 474 TYR 0.017 0.001 TYR A 460 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 0.85453 ( 3) hydrogen bonds : bond 0.03677 ( 274) hydrogen bonds : angle 4.28137 ( 816) SS BOND : bond 0.00109 ( 1) SS BOND : angle 1.42697 ( 2) covalent geometry : bond 0.00265 ( 4579) covalent geometry : angle 0.48376 ( 6197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7077 (ttm) REVERT: A 176 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8133 (mtp) REVERT: A 292 ILE cc_start: 0.7995 (mm) cc_final: 0.7748 (mt) REVERT: A 309 MET cc_start: 0.7652 (mmp) cc_final: 0.7224 (mmp) REVERT: A 321 ASN cc_start: 0.8103 (t0) cc_final: 0.7609 (t0) REVERT: A 351 MET cc_start: 0.8431 (mtp) cc_final: 0.8092 (mtm) REVERT: A 427 ARG cc_start: 0.6768 (mtm180) cc_final: 0.6094 (mtm180) REVERT: A 494 ASP cc_start: 0.8638 (t70) cc_final: 0.8364 (t0) REVERT: A 577 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7507 (tppt) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.1743 time to fit residues: 14.7081 Evaluate side-chains 63 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.121642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095637 restraints weight = 5599.165| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.69 r_work: 0.2838 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4581 Z= 0.126 Angle : 0.496 7.006 6202 Z= 0.249 Chirality : 0.038 0.127 677 Planarity : 0.004 0.032 745 Dihedral : 5.325 38.777 698 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.96 % Allowed : 12.61 % Favored : 85.43 % 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: 1.38 (0.36), residues: 541 helix: 1.81 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE A 404 TYR 0.024 0.001 TYR A 460 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 0.82245 ( 3) hydrogen bonds : bond 0.03728 ( 274) hydrogen bonds : angle 4.28416 ( 816) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.48111 ( 2) covalent geometry : bond 0.00297 ( 4579) covalent geometry : angle 0.49468 ( 6197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7279 (ttm) REVERT: A 176 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: A 292 ILE cc_start: 0.8259 (mm) cc_final: 0.8054 (mt) REVERT: A 321 ASN cc_start: 0.8229 (t0) cc_final: 0.7774 (t0) REVERT: A 427 ARG cc_start: 0.6975 (mtm180) cc_final: 0.6288 (mtm180) REVERT: A 577 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7645 (tppt) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.1431 time to fit residues: 11.6931 Evaluate side-chains 62 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.121899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095947 restraints weight = 5536.958| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.68 r_work: 0.2841 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4581 Z= 0.127 Angle : 0.493 6.541 6202 Z= 0.248 Chirality : 0.038 0.123 677 Planarity : 0.004 0.032 745 Dihedral : 5.341 38.725 698 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.96 % Allowed : 13.04 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.36), residues: 541 helix: 1.82 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE A 474 TYR 0.023 0.001 TYR A 460 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 0.83494 ( 3) hydrogen bonds : bond 0.03706 ( 274) hydrogen bonds : angle 4.25114 ( 816) SS BOND : bond 0.00088 ( 1) SS BOND : angle 1.40993 ( 2) covalent geometry : bond 0.00300 ( 4579) covalent geometry : angle 0.49239 ( 6197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7238 (ttm) REVERT: A 176 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: A 292 ILE cc_start: 0.8270 (mm) cc_final: 0.8064 (mt) REVERT: A 309 MET cc_start: 0.7830 (mmt) cc_final: 0.7395 (mmp) REVERT: A 321 ASN cc_start: 0.8239 (t0) cc_final: 0.7787 (t0) REVERT: A 427 ARG cc_start: 0.6963 (mtm180) cc_final: 0.6266 (mtm180) REVERT: A 494 ASP cc_start: 0.8673 (t70) cc_final: 0.8434 (t0) REVERT: A 577 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7664 (tppt) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.1401 time to fit residues: 11.5613 Evaluate side-chains 62 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 52 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 0.0020 chunk 45 optimal weight: 0.6980 overall best weight: 0.1904 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.126423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098775 restraints weight = 5559.050| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.85 r_work: 0.2873 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4581 Z= 0.094 Angle : 0.472 6.290 6202 Z= 0.237 Chirality : 0.037 0.124 677 Planarity : 0.003 0.031 745 Dihedral : 4.957 38.444 698 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 13.70 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.36), residues: 541 helix: 2.05 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.35 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 PHE 0.010 0.001 PHE A 404 TYR 0.019 0.001 TYR A 460 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 0.86208 ( 3) hydrogen bonds : bond 0.03340 ( 274) hydrogen bonds : angle 4.12364 ( 816) SS BOND : bond 0.00108 ( 1) SS BOND : angle 1.13471 ( 2) covalent geometry : bond 0.00201 ( 4579) covalent geometry : angle 0.47150 ( 6197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7077 (ttm) REVERT: A 176 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: A 292 ILE cc_start: 0.8071 (mm) cc_final: 0.7869 (mt) REVERT: A 309 MET cc_start: 0.7549 (mmt) cc_final: 0.7238 (mmp) REVERT: A 321 ASN cc_start: 0.8190 (t0) cc_final: 0.7713 (t0) REVERT: A 427 ARG cc_start: 0.6888 (mtm180) cc_final: 0.6190 (mtm180) REVERT: A 494 ASP cc_start: 0.8637 (t70) cc_final: 0.8371 (t0) REVERT: A 577 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7522 (tppt) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.1776 time to fit residues: 15.6960 Evaluate side-chains 63 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.121486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095671 restraints weight = 5519.255| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.66 r_work: 0.2842 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4581 Z= 0.150 Angle : 0.508 6.219 6202 Z= 0.256 Chirality : 0.039 0.125 677 Planarity : 0.004 0.031 745 Dihedral : 5.310 39.056 698 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.09 % Allowed : 14.13 % Favored : 84.78 % 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: 1.51 (0.36), residues: 541 helix: 1.91 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.33 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.014 0.001 PHE A 474 TYR 0.021 0.001 TYR A 460 ARG 0.001 0.000 ARG A 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 0.81383 ( 3) hydrogen bonds : bond 0.03740 ( 274) hydrogen bonds : angle 4.24846 ( 816) SS BOND : bond 0.00062 ( 1) SS BOND : angle 1.46446 ( 2) covalent geometry : bond 0.00366 ( 4579) covalent geometry : angle 0.50723 ( 6197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7183 (ttm) REVERT: A 176 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: A 309 MET cc_start: 0.7791 (mmt) cc_final: 0.7404 (mmp) REVERT: A 321 ASN cc_start: 0.8242 (t0) cc_final: 0.7783 (t0) REVERT: A 427 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6324 (mtm180) REVERT: A 494 ASP cc_start: 0.8668 (t70) cc_final: 0.8430 (t0) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.1371 time to fit residues: 10.7243 Evaluate side-chains 58 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 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 = 0.3291 r_free = 0.3291 target = 0.121694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095603 restraints weight = 5576.677| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.69 r_work: 0.2837 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4581 Z= 0.142 Angle : 0.506 6.212 6202 Z= 0.255 Chirality : 0.038 0.125 677 Planarity : 0.004 0.032 745 Dihedral : 5.431 42.885 698 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 14.13 % Favored : 84.57 % 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: 1.46 (0.36), residues: 541 helix: 1.87 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.013 0.001 PHE A 474 TYR 0.022 0.001 TYR A 460 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 1) link_NAG-ASN : angle 0.83128 ( 3) hydrogen bonds : bond 0.03731 ( 274) hydrogen bonds : angle 4.26015 ( 816) SS BOND : bond 0.00094 ( 1) SS BOND : angle 1.43774 ( 2) covalent geometry : bond 0.00344 ( 4579) covalent geometry : angle 0.50550 ( 6197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.73 seconds wall clock time: 45 minutes 2.59 seconds (2702.59 seconds total)