Starting phenix.real_space_refine on Wed Jul 23 08:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8di5_27439/07_2025/8di5_27439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8di5_27439/07_2025/8di5_27439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2025/8di5_27439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2025/8di5_27439.map" model { file = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2025/8di5_27439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2025/8di5_27439.cif" } resolution = 3.04 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= 0.014 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 12 5.16 5 C 1573 2.51 5 N 409 2.21 5 O 473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 2467 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.21, per 1000 atoms: 1.30 Number of scatterers: 2467 At special positions: 0 Unit cell: (68, 79, 73, 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 12 16.00 O 473 8.00 N 409 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " 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 C1301 " - " ASN C 343 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 281.4 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 5 sheets defined 15.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.008A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.962A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.065A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.268A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU H 33 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 80 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.64 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: 786 1.34 - 1.46: 698 1.46 - 1.58: 1036 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 2534 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.39e+00 bond pdb=" CB ILE C 472 " pdb=" CG2 ILE C 472 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CB ASN H 83 " pdb=" CG ASN H 83 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CG LEU C 452 " pdb=" CD1 LEU C 452 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.67e+00 ... (remaining 2529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 3417 3.77 - 7.54: 26 7.54 - 11.31: 3 11.31 - 15.08: 0 15.08 - 18.85: 1 Bond angle restraints: 3447 Sorted by residual: angle pdb=" CA LEU C 518 " pdb=" CB LEU C 518 " pdb=" CG LEU C 518 " ideal model delta sigma weight residual 116.30 135.15 -18.85 3.50e+00 8.16e-02 2.90e+01 angle pdb=" C GLU H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta sigma weight residual 122.87 118.15 4.72 1.61e+00 3.86e-01 8.60e+00 angle pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta sigma weight residual 122.68 126.77 -4.09 1.47e+00 4.63e-01 7.72e+00 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CA TYR C 473 " pdb=" CB TYR C 473 " pdb=" CG TYR C 473 " ideal model delta sigma weight residual 113.90 118.55 -4.65 1.80e+00 3.09e-01 6.69e+00 ... (remaining 3442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1332 15.12 - 30.23: 130 30.23 - 45.35: 23 45.35 - 60.47: 3 60.47 - 75.58: 2 Dihedral angle restraints: 1490 sinusoidal: 589 harmonic: 901 Sorted by residual: dihedral pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 62.46 30.54 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 207 0.038 - 0.077: 95 0.077 - 0.115: 37 0.115 - 0.154: 22 0.154 - 0.192: 3 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LEU C 518 " pdb=" N LEU C 518 " pdb=" C LEU C 518 " pdb=" CB LEU C 518 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 361 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 521 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 362 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL C 362 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 362 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 363 " -0.011 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 757 2.82 - 3.34: 1959 3.34 - 3.86: 4099 3.86 - 4.38: 4610 4.38 - 4.90: 8120 Nonbonded interactions: 19545 Sorted by model distance: nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.300 3.040 nonbonded pdb=" O ASN C 481 " pdb=" NE2 GLN H 39 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.364 3.040 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.390 3.120 nonbonded pdb=" OG SER H 117 " pdb=" N SER H 118 " model vdw 2.392 3.120 ... (remaining 19540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.440 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.049 2540 Z= 0.266 Angle : 0.954 18.847 3460 Z= 0.483 Chirality : 0.057 0.192 364 Planarity : 0.007 0.057 447 Dihedral : 12.401 75.582 907 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % 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: -2.40 (0.41), residues: 307 helix: -4.35 (0.46), residues: 33 sheet: 0.00 (0.51), residues: 90 loop : -1.97 (0.37), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.032 0.004 PHE C 347 TYR 0.028 0.003 TYR C 495 ARG 0.003 0.001 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 1) link_NAG-ASN : angle 1.96518 ( 3) hydrogen bonds : bond 0.17742 ( 75) hydrogen bonds : angle 9.94340 ( 204) SS BOND : bond 0.00324 ( 5) SS BOND : angle 1.25721 ( 10) covalent geometry : bond 0.00606 ( 2534) covalent geometry : angle 0.95118 ( 3447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.8481 (mmtp) cc_final: 0.7351 (ttpt) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2029 time to fit residues: 19.1547 Evaluate side-chains 68 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095659 restraints weight = 4265.631| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.93 r_work: 0.3136 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2540 Z= 0.176 Angle : 0.629 11.381 3460 Z= 0.322 Chirality : 0.043 0.157 364 Planarity : 0.005 0.039 447 Dihedral : 5.640 26.047 369 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.26 % Allowed : 12.08 % Favored : 85.66 % 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: -1.99 (0.43), residues: 307 helix: -3.41 (0.62), residues: 34 sheet: 0.17 (0.53), residues: 90 loop : -1.74 (0.40), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.023 0.002 PHE C 456 TYR 0.019 0.001 TYR C 495 ARG 0.003 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 1) link_NAG-ASN : angle 1.82549 ( 3) hydrogen bonds : bond 0.03849 ( 75) hydrogen bonds : angle 7.44342 ( 204) SS BOND : bond 0.00378 ( 5) SS BOND : angle 0.74173 ( 10) covalent geometry : bond 0.00391 ( 2534) covalent geometry : angle 0.62692 ( 3447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.285 Fit side-chains REVERT: C 386 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7350 (ttpt) REVERT: C 403 ARG cc_start: 0.8730 (ptt180) cc_final: 0.8387 (ptm-80) REVERT: H 22 CYS cc_start: 0.7170 (t) cc_final: 0.6937 (t) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.2225 time to fit residues: 19.4224 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094421 restraints weight = 4320.372| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.05 r_work: 0.3128 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2540 Z= 0.164 Angle : 0.583 10.034 3460 Z= 0.300 Chirality : 0.043 0.149 364 Planarity : 0.004 0.034 447 Dihedral : 5.165 25.232 369 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 14.34 % Favored : 83.40 % 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 (0.45), residues: 307 helix: -3.04 (0.78), residues: 34 sheet: 0.35 (0.52), residues: 90 loop : -1.58 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.018 0.002 PHE C 456 TYR 0.019 0.001 TYR C 495 ARG 0.001 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 1) link_NAG-ASN : angle 1.69232 ( 3) hydrogen bonds : bond 0.03435 ( 75) hydrogen bonds : angle 6.73853 ( 204) SS BOND : bond 0.00161 ( 5) SS BOND : angle 0.48386 ( 10) covalent geometry : bond 0.00364 ( 2534) covalent geometry : angle 0.58134 ( 3447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.279 Fit side-chains REVERT: C 378 LYS cc_start: 0.8801 (mttm) cc_final: 0.8560 (mtpt) REVERT: C 386 LYS cc_start: 0.8476 (mmtp) cc_final: 0.7322 (ttpt) REVERT: H 22 CYS cc_start: 0.7182 (t) cc_final: 0.6926 (t) REVERT: H 79 TYR cc_start: 0.8019 (m-10) cc_final: 0.7652 (m-10) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.2251 time to fit residues: 20.1519 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094967 restraints weight = 4327.786| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.07 r_work: 0.3126 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2540 Z= 0.135 Angle : 0.550 8.688 3460 Z= 0.284 Chirality : 0.043 0.140 364 Planarity : 0.004 0.034 447 Dihedral : 4.924 24.115 369 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.26 % Allowed : 16.23 % Favored : 81.51 % 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: -1.49 (0.46), residues: 307 helix: -3.00 (0.81), residues: 34 sheet: 0.78 (0.55), residues: 82 loop : -1.48 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.015 0.001 PHE C 456 TYR 0.017 0.001 TYR C 495 ARG 0.001 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 1) link_NAG-ASN : angle 1.50912 ( 3) hydrogen bonds : bond 0.03229 ( 75) hydrogen bonds : angle 6.48617 ( 204) SS BOND : bond 0.00177 ( 5) SS BOND : angle 0.38704 ( 10) covalent geometry : bond 0.00299 ( 2534) covalent geometry : angle 0.54844 ( 3447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.361 Fit side-chains REVERT: C 378 LYS cc_start: 0.8791 (mttm) cc_final: 0.8533 (mtpt) REVERT: C 386 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7309 (ttpt) REVERT: C 501 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: H 22 CYS cc_start: 0.7356 (t) cc_final: 0.7116 (t) REVERT: H 72 ASP cc_start: 0.8537 (t0) cc_final: 0.8214 (t0) REVERT: H 79 TYR cc_start: 0.7972 (m-10) cc_final: 0.7606 (m-10) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.2194 time to fit residues: 18.9069 Evaluate side-chains 73 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092671 restraints weight = 4366.488| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.02 r_work: 0.3101 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2540 Z= 0.179 Angle : 0.574 8.361 3460 Z= 0.297 Chirality : 0.044 0.141 364 Planarity : 0.004 0.035 447 Dihedral : 5.065 24.494 369 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.40 % Allowed : 15.85 % Favored : 80.75 % 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: -1.48 (0.46), residues: 307 helix: -3.07 (0.79), residues: 34 sheet: 0.54 (0.52), residues: 88 loop : -1.39 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.010 0.001 PHE C 347 TYR 0.019 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 1) link_NAG-ASN : angle 1.57686 ( 3) hydrogen bonds : bond 0.03407 ( 75) hydrogen bonds : angle 6.42593 ( 204) SS BOND : bond 0.00168 ( 5) SS BOND : angle 0.44729 ( 10) covalent geometry : bond 0.00403 ( 2534) covalent geometry : angle 0.57299 ( 3447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.272 Fit side-chains REVERT: C 378 LYS cc_start: 0.8799 (mttm) cc_final: 0.8537 (mtpt) REVERT: C 386 LYS cc_start: 0.8500 (mmtp) cc_final: 0.7431 (ttpt) REVERT: C 403 ARG cc_start: 0.8671 (ptt180) cc_final: 0.8443 (ptt180) REVERT: H 19 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8407 (ttm110) REVERT: H 22 CYS cc_start: 0.7283 (t) cc_final: 0.7062 (t) REVERT: H 72 ASP cc_start: 0.8464 (t0) cc_final: 0.8032 (t0) REVERT: H 79 TYR cc_start: 0.7963 (m-10) cc_final: 0.7592 (m-10) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 0.2212 time to fit residues: 19.7934 Evaluate side-chains 75 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093934 restraints weight = 4347.758| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.99 r_work: 0.3120 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2540 Z= 0.146 Angle : 0.548 7.933 3460 Z= 0.286 Chirality : 0.043 0.137 364 Planarity : 0.004 0.034 447 Dihedral : 4.973 24.315 369 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.64 % Allowed : 17.74 % Favored : 79.62 % 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: -1.36 (0.47), residues: 307 helix: -3.06 (0.93), residues: 27 sheet: 0.59 (0.52), residues: 88 loop : -1.36 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.011 0.001 PHE C 456 TYR 0.018 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 1) link_NAG-ASN : angle 1.59928 ( 3) hydrogen bonds : bond 0.03169 ( 75) hydrogen bonds : angle 6.34519 ( 204) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.41570 ( 10) covalent geometry : bond 0.00327 ( 2534) covalent geometry : angle 0.54607 ( 3447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.291 Fit side-chains REVERT: C 378 LYS cc_start: 0.8795 (mttm) cc_final: 0.8522 (mtpt) REVERT: C 386 LYS cc_start: 0.8484 (mmtp) cc_final: 0.7431 (ttpt) REVERT: C 403 ARG cc_start: 0.8677 (ptt180) cc_final: 0.8452 (ptt180) REVERT: C 405 ASP cc_start: 0.8282 (p0) cc_final: 0.8076 (p0) REVERT: H 19 ARG cc_start: 0.8673 (ttm110) cc_final: 0.8130 (ttm110) REVERT: H 22 CYS cc_start: 0.7259 (t) cc_final: 0.7035 (t) REVERT: H 72 ASP cc_start: 0.8428 (t0) cc_final: 0.8030 (t0) REVERT: H 81 GLN cc_start: 0.8072 (tt0) cc_final: 0.7535 (tt0) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.2110 time to fit residues: 18.0492 Evaluate side-chains 74 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092472 restraints weight = 4494.560| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.02 r_work: 0.3101 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2540 Z= 0.186 Angle : 0.566 7.732 3460 Z= 0.296 Chirality : 0.044 0.137 364 Planarity : 0.004 0.036 447 Dihedral : 5.070 24.629 369 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.40 % Allowed : 16.98 % Favored : 79.62 % 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: -1.44 (0.46), residues: 307 helix: -3.15 (0.77), residues: 34 sheet: 0.50 (0.52), residues: 88 loop : -1.29 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.000 0.000 HIS C 519 PHE 0.019 0.002 PHE H 27 TYR 0.019 0.002 TYR C 495 ARG 0.001 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 1) link_NAG-ASN : angle 1.61579 ( 3) hydrogen bonds : bond 0.03313 ( 75) hydrogen bonds : angle 6.36011 ( 204) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.46916 ( 10) covalent geometry : bond 0.00419 ( 2534) covalent geometry : angle 0.56486 ( 3447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8792 (mttm) cc_final: 0.8536 (mtpt) REVERT: C 386 LYS cc_start: 0.8522 (mmtp) cc_final: 0.7470 (ttpt) REVERT: C 403 ARG cc_start: 0.8640 (ptt180) cc_final: 0.8380 (ptt180) REVERT: C 405 ASP cc_start: 0.8348 (p0) cc_final: 0.8132 (p0) REVERT: C 467 ASP cc_start: 0.8528 (t0) cc_final: 0.8320 (t0) REVERT: H 19 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8363 (ttm110) REVERT: H 22 CYS cc_start: 0.7256 (t) cc_final: 0.7033 (t) REVERT: H 72 ASP cc_start: 0.8395 (t0) cc_final: 0.8003 (t0) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.2262 time to fit residues: 19.9731 Evaluate side-chains 79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094206 restraints weight = 4369.661| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.05 r_work: 0.3124 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2540 Z= 0.134 Angle : 0.545 7.578 3460 Z= 0.283 Chirality : 0.043 0.136 364 Planarity : 0.003 0.035 447 Dihedral : 4.890 24.167 369 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.64 % Allowed : 17.74 % Favored : 79.62 % 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: -1.37 (0.46), residues: 307 helix: -3.04 (0.93), residues: 27 sheet: 0.53 (0.52), residues: 88 loop : -1.34 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.019 0.001 PHE H 27 TYR 0.016 0.001 TYR C 495 ARG 0.002 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 1) link_NAG-ASN : angle 1.60942 ( 3) hydrogen bonds : bond 0.03101 ( 75) hydrogen bonds : angle 6.25122 ( 204) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.34725 ( 10) covalent geometry : bond 0.00301 ( 2534) covalent geometry : angle 0.54356 ( 3447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8790 (mttm) cc_final: 0.8500 (mtpt) REVERT: C 386 LYS cc_start: 0.8459 (mmtp) cc_final: 0.7439 (ttpt) REVERT: C 403 ARG cc_start: 0.8640 (ptt180) cc_final: 0.8388 (ptt180) REVERT: C 405 ASP cc_start: 0.8392 (p0) cc_final: 0.8182 (p0) REVERT: H 19 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8396 (ttm110) REVERT: H 22 CYS cc_start: 0.7224 (t) cc_final: 0.6982 (t) REVERT: H 72 ASP cc_start: 0.8376 (t0) cc_final: 0.7989 (t0) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.2361 time to fit residues: 20.2903 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094309 restraints weight = 4334.685| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.02 r_work: 0.3125 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2540 Z= 0.142 Angle : 0.550 7.383 3460 Z= 0.286 Chirality : 0.043 0.136 364 Planarity : 0.004 0.038 447 Dihedral : 4.862 23.466 369 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.64 % Allowed : 18.87 % Favored : 78.49 % 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 (0.46), residues: 307 helix: -3.08 (0.92), residues: 27 sheet: 0.57 (0.52), residues: 88 loop : -1.28 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.019 0.001 PHE H 27 TYR 0.017 0.001 TYR C 495 ARG 0.003 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 1.55641 ( 3) hydrogen bonds : bond 0.03129 ( 75) hydrogen bonds : angle 6.18433 ( 204) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.36588 ( 10) covalent geometry : bond 0.00320 ( 2534) covalent geometry : angle 0.54842 ( 3447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8785 (mttm) cc_final: 0.8502 (mtpt) REVERT: C 386 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7434 (ttpt) REVERT: C 403 ARG cc_start: 0.8652 (ptt180) cc_final: 0.8400 (ptt180) REVERT: C 405 ASP cc_start: 0.8403 (p0) cc_final: 0.8188 (p0) REVERT: H 19 ARG cc_start: 0.8715 (ttm110) cc_final: 0.8353 (ttm110) REVERT: H 22 CYS cc_start: 0.7209 (t) cc_final: 0.6968 (t) REVERT: H 72 ASP cc_start: 0.8357 (t0) cc_final: 0.7959 (t0) REVERT: H 79 TYR cc_start: 0.8076 (m-10) cc_final: 0.7780 (m-10) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.2306 time to fit residues: 19.3245 Evaluate side-chains 76 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093486 restraints weight = 4322.785| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.03 r_work: 0.3114 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2540 Z= 0.169 Angle : 0.565 7.346 3460 Z= 0.295 Chirality : 0.043 0.135 364 Planarity : 0.003 0.035 447 Dihedral : 4.973 24.088 369 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 18.87 % Favored : 78.49 % 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: -1.34 (0.46), residues: 307 helix: -3.04 (0.95), residues: 27 sheet: 0.50 (0.52), residues: 88 loop : -1.29 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.017 0.002 PHE H 27 TYR 0.017 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 1) link_NAG-ASN : angle 1.64135 ( 3) hydrogen bonds : bond 0.03250 ( 75) hydrogen bonds : angle 6.22029 ( 204) SS BOND : bond 0.00139 ( 5) SS BOND : angle 0.39376 ( 10) covalent geometry : bond 0.00380 ( 2534) covalent geometry : angle 0.56325 ( 3447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.270 Fit side-chains REVERT: C 378 LYS cc_start: 0.8780 (mttm) cc_final: 0.8501 (mtpt) REVERT: C 386 LYS cc_start: 0.8506 (mmtp) cc_final: 0.7440 (ttpt) REVERT: C 403 ARG cc_start: 0.8671 (ptt180) cc_final: 0.8417 (ptt180) REVERT: C 405 ASP cc_start: 0.8396 (p0) cc_final: 0.8177 (p0) REVERT: H 19 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8131 (ttm110) REVERT: H 22 CYS cc_start: 0.7243 (t) cc_final: 0.7006 (t) REVERT: H 72 ASP cc_start: 0.8377 (t0) cc_final: 0.7985 (t0) REVERT: H 79 TYR cc_start: 0.8078 (m-10) cc_final: 0.7775 (m-10) REVERT: H 81 GLN cc_start: 0.8097 (tt0) cc_final: 0.7502 (tt0) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.2213 time to fit residues: 18.5498 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093189 restraints weight = 4395.848| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.99 r_work: 0.3108 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2540 Z= 0.171 Angle : 0.568 7.256 3460 Z= 0.297 Chirality : 0.043 0.136 364 Planarity : 0.003 0.035 447 Dihedral : 4.987 24.604 369 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.64 % Allowed : 19.62 % Favored : 77.74 % 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: -1.32 (0.46), residues: 307 helix: -3.15 (0.78), residues: 34 sheet: 0.53 (0.52), residues: 88 loop : -1.16 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.017 0.002 PHE H 27 TYR 0.018 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 1.62331 ( 3) hydrogen bonds : bond 0.03254 ( 75) hydrogen bonds : angle 6.22482 ( 204) SS BOND : bond 0.00143 ( 5) SS BOND : angle 0.39711 ( 10) covalent geometry : bond 0.00386 ( 2534) covalent geometry : angle 0.56644 ( 3447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.26 seconds wall clock time: 32 minutes 54.54 seconds (1974.54 seconds total)