Starting phenix.real_space_refine on Wed Mar 5 16:04:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dly_27520/03_2025/8dly_27520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/03_2025/8dly_27520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_2025/8dly_27520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_2025/8dly_27520.map" model { file = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_2025/8dly_27520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_2025/8dly_27520.cif" } resolution = 3.0 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= -0.002 sd= 0.032 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 13 5.16 5 C 1582 2.51 5 N 417 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2483 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: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} 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: 2.75, per 1000 atoms: 1.11 Number of scatterers: 2483 At special positions: 0 Unit cell: (68, 82, 69, 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 13 16.00 O 471 8.00 N 417 7.00 C 1582 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=2.02 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: 0.52 Conformation dependent library (CDL) restraints added in 266.3 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 28.3% 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 370 removed outlier: 3.619A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.081A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.330A 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 86 through 90 removed outlier: 3.505A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.660A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.815A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.124A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 186 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: 0.57 Time building geometry restraints manager: 0.65 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: 783 1.34 - 1.46: 649 1.46 - 1.58: 1102 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2550 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" CB ASN H 50 " pdb=" CG ASN H 50 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.19e-02 7.06e+03 2.32e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3270 1.92 - 3.84: 172 3.84 - 5.76: 21 5.76 - 7.68: 4 7.68 - 9.60: 2 Bond angle restraints: 3469 Sorted by residual: angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" C GLY C 476 " pdb=" N SER C 477 " pdb=" CA SER C 477 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.78e+00 angle pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta sigma weight residual 120.38 124.48 -4.10 1.37e+00 5.33e-01 8.95e+00 angle pdb=" N LEU C 518 " pdb=" CA LEU C 518 " pdb=" C LEU C 518 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 125.90 -9.60 3.50e+00 8.16e-02 7.52e+00 ... (remaining 3464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 1306 13.75 - 27.50: 146 27.50 - 41.25: 38 41.25 - 54.99: 9 54.99 - 68.74: 1 Dihedral angle restraints: 1500 sinusoidal: 593 harmonic: 907 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 126.09 -33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual 180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CG ARG C 509 " pdb=" CD ARG C 509 " pdb=" NE ARG C 509 " pdb=" CZ ARG C 509 " ideal model delta sinusoidal sigma weight residual -90.00 -131.99 41.99 2 1.50e+01 4.44e-03 9.55e+00 ... (remaining 1497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 224 0.046 - 0.093: 100 0.093 - 0.139: 38 0.139 - 0.185: 5 0.185 - 0.231: 3 Chirality restraints: 370 Sorted by residual: chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA MET H 106 " pdb=" N MET H 106 " pdb=" C MET H 106 " pdb=" CB MET H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 367 not shown) Planarity restraints: 449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 520 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA C 520 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 520 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO C 521 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN H 60 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO H 61 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 41 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.025 5.00e-02 4.00e+02 ... (remaining 446 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 789 2.83 - 3.35: 1927 3.35 - 3.87: 4036 3.87 - 4.38: 4493 4.38 - 4.90: 8057 Nonbonded interactions: 19302 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.317 3.040 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.432 3.120 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.487 3.120 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.505 3.040 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.524 3.040 ... (remaining 19297 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: 2.550 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: 0.010 Set scattering table: 0.020 Process input model: 11.470 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 2550 Z= 0.329 Angle : 0.939 9.601 3469 Z= 0.512 Chirality : 0.059 0.231 370 Planarity : 0.006 0.053 448 Dihedral : 12.405 68.742 913 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.37 % Allowed : 3.00 % Favored : 96.63 % 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 (0.40), residues: 310 helix: -3.94 (0.60), residues: 26 sheet: -0.08 (0.45), residues: 104 loop : -1.03 (0.37), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 47 HIS 0.011 0.003 HIS H 35 PHE 0.017 0.002 PHE H 27 TYR 0.015 0.002 TYR C 453 ARG 0.007 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.257 Fit side-chains REVERT: C 420 ASP cc_start: 0.8522 (m-30) cc_final: 0.8206 (m-30) REVERT: C 424 LYS cc_start: 0.8840 (tptt) cc_final: 0.8594 (tppp) REVERT: C 456 PHE cc_start: 0.8663 (t80) cc_final: 0.8216 (t80) REVERT: C 474 GLN cc_start: 0.7637 (mt0) cc_final: 0.7419 (mt0) REVERT: H 39 GLN cc_start: 0.7728 (pt0) cc_final: 0.7151 (pm20) REVERT: H 86 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6622 (mtp180) REVERT: H 92 ILE cc_start: 0.8541 (mt) cc_final: 0.7759 (mm) outliers start: 1 outliers final: 2 residues processed: 100 average time/residue: 1.1402 time to fit residues: 116.4591 Evaluate side-chains 63 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN C 506 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076829 restraints weight = 5947.263| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.17 r_work: 0.3109 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2550 Z= 0.187 Angle : 0.596 6.518 3469 Z= 0.295 Chirality : 0.044 0.140 370 Planarity : 0.004 0.032 448 Dihedral : 8.726 124.730 377 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.75 % Allowed : 16.85 % Favored : 79.40 % 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: -0.97 (0.42), residues: 310 helix: -3.58 (0.75), residues: 26 sheet: 0.11 (0.48), residues: 98 loop : -0.56 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS C 519 PHE 0.006 0.001 PHE H 29 TYR 0.014 0.001 TYR H 79 ARG 0.005 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8675 (ptm-80) cc_final: 0.8386 (ptm-80) REVERT: C 420 ASP cc_start: 0.8734 (m-30) cc_final: 0.8478 (m-30) REVERT: C 424 LYS cc_start: 0.8985 (tptt) cc_final: 0.8712 (tppp) REVERT: C 456 PHE cc_start: 0.8895 (t80) cc_final: 0.8406 (t80) REVERT: H 29 PHE cc_start: 0.8492 (t80) cc_final: 0.8201 (t80) REVERT: H 60 ASN cc_start: 0.9028 (t0) cc_final: 0.8799 (t0) REVERT: H 86 ARG cc_start: 0.7330 (mtp180) cc_final: 0.6586 (mtp180) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 1.2113 time to fit residues: 96.5302 Evaluate side-chains 69 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075067 restraints weight = 5841.901| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.24 r_work: 0.3091 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2550 Z= 0.223 Angle : 0.587 6.381 3469 Z= 0.296 Chirality : 0.044 0.134 370 Planarity : 0.004 0.033 448 Dihedral : 5.307 44.479 375 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.62 % Allowed : 18.35 % Favored : 76.03 % 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: -1.00 (0.43), residues: 310 helix: -3.48 (1.03), residues: 20 sheet: 0.12 (0.47), residues: 103 loop : -0.76 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE C 347 TYR 0.010 0.001 TYR C 495 ARG 0.007 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8669 (m-30) cc_final: 0.8394 (m-30) REVERT: C 424 LYS cc_start: 0.9001 (tptt) cc_final: 0.8729 (tppp) REVERT: C 444 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8109 (mtmm) REVERT: H 60 ASN cc_start: 0.8991 (t0) cc_final: 0.8769 (t0) REVERT: H 86 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6649 (mtp180) REVERT: H 88 GLU cc_start: 0.9003 (pp20) cc_final: 0.8730 (pp20) REVERT: H 89 ASP cc_start: 0.8043 (m-30) cc_final: 0.7776 (m-30) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 1.1580 time to fit residues: 87.6560 Evaluate side-chains 68 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.075795 restraints weight = 5923.459| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.17 r_work: 0.3086 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2550 Z= 0.199 Angle : 0.569 6.991 3469 Z= 0.283 Chirality : 0.043 0.134 370 Planarity : 0.004 0.034 448 Dihedral : 5.061 42.759 373 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.87 % Allowed : 20.22 % Favored : 74.91 % 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: -0.97 (0.43), residues: 310 helix: -3.28 (1.11), residues: 20 sheet: 0.05 (0.47), residues: 105 loop : -0.71 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE C 347 TYR 0.009 0.001 TYR C 495 ARG 0.010 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8641 (m-30) cc_final: 0.8370 (m-30) REVERT: C 424 LYS cc_start: 0.8995 (tptt) cc_final: 0.8722 (tppp) REVERT: C 444 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8099 (mtmm) REVERT: H 29 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7218 (t80) REVERT: H 37 VAL cc_start: 0.9269 (t) cc_final: 0.9067 (m) REVERT: H 60 ASN cc_start: 0.8990 (t0) cc_final: 0.8787 (t0) REVERT: H 74 SER cc_start: 0.9192 (m) cc_final: 0.8919 (t) REVERT: H 86 ARG cc_start: 0.7304 (mtp180) cc_final: 0.6569 (mtp180) REVERT: H 88 GLU cc_start: 0.9035 (pp20) cc_final: 0.8668 (pp20) REVERT: H 89 ASP cc_start: 0.8088 (m-30) cc_final: 0.7819 (m-30) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 1.2396 time to fit residues: 92.4964 Evaluate side-chains 72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073963 restraints weight = 5962.143| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.28 r_work: 0.3061 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2550 Z= 0.237 Angle : 0.591 7.620 3469 Z= 0.293 Chirality : 0.044 0.133 370 Planarity : 0.004 0.033 448 Dihedral : 5.077 44.485 373 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.62 % Allowed : 21.35 % Favored : 73.03 % 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: -0.91 (0.44), residues: 310 helix: -3.11 (1.18), residues: 20 sheet: -0.03 (0.46), residues: 110 loop : -0.62 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.007 0.001 PHE C 347 TYR 0.010 0.001 TYR C 495 ARG 0.009 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8664 (ttm-80) REVERT: C 420 ASP cc_start: 0.8617 (m-30) cc_final: 0.8329 (m-30) REVERT: C 424 LYS cc_start: 0.8981 (tptt) cc_final: 0.8633 (tppp) REVERT: C 444 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8124 (mtmm) REVERT: H 39 GLN cc_start: 0.8026 (pt0) cc_final: 0.7653 (tt0) REVERT: H 60 ASN cc_start: 0.9005 (t0) cc_final: 0.8804 (t0) REVERT: H 74 SER cc_start: 0.9202 (m) cc_final: 0.8930 (t) REVERT: H 86 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6586 (mtp180) REVERT: H 88 GLU cc_start: 0.9053 (pp20) cc_final: 0.8616 (pp20) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 1.1664 time to fit residues: 88.3270 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070987 restraints weight = 5979.151| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.19 r_work: 0.3001 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 2550 Z= 0.408 Angle : 0.657 8.262 3469 Z= 0.331 Chirality : 0.046 0.139 370 Planarity : 0.004 0.029 448 Dihedral : 5.642 49.124 373 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.37 % Allowed : 21.72 % Favored : 71.91 % 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: -1.23 (0.44), residues: 310 helix: -2.98 (0.99), residues: 26 sheet: -0.25 (0.47), residues: 107 loop : -0.77 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 353 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE C 347 TYR 0.013 0.001 TYR C 495 ARG 0.007 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: C 424 LYS cc_start: 0.8981 (tptt) cc_final: 0.8614 (tppp) REVERT: C 444 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8136 (mtmm) REVERT: C 516 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6697 (tm-30) REVERT: H 39 GLN cc_start: 0.8133 (pt0) cc_final: 0.7720 (tt0) REVERT: H 74 SER cc_start: 0.9292 (m) cc_final: 0.9020 (t) REVERT: H 86 ARG cc_start: 0.7336 (mtp180) cc_final: 0.6705 (mtp180) REVERT: H 88 GLU cc_start: 0.9009 (pp20) cc_final: 0.8561 (pp20) REVERT: H 89 ASP cc_start: 0.8286 (m-30) cc_final: 0.7916 (m-30) outliers start: 17 outliers final: 10 residues processed: 74 average time/residue: 1.1637 time to fit residues: 88.1052 Evaluate side-chains 74 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073014 restraints weight = 6018.014| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.27 r_work: 0.3036 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2550 Z= 0.245 Angle : 0.643 8.495 3469 Z= 0.314 Chirality : 0.045 0.140 370 Planarity : 0.004 0.035 448 Dihedral : 5.325 45.415 373 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.62 % Allowed : 22.47 % Favored : 71.91 % 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: -1.28 (0.44), residues: 310 helix: -2.96 (0.97), residues: 26 sheet: -0.40 (0.45), residues: 110 loop : -0.73 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE H 29 TYR 0.009 0.001 TYR C 495 ARG 0.008 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8536 (ttp80) REVERT: C 408 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.8450 (ptm-80) REVERT: C 424 LYS cc_start: 0.8969 (tptt) cc_final: 0.8644 (tppp) REVERT: C 444 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8114 (mtmm) REVERT: C 516 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6817 (tm-30) REVERT: H 39 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: H 74 SER cc_start: 0.9258 (m) cc_final: 0.8999 (t) REVERT: H 86 ARG cc_start: 0.7287 (mtp180) cc_final: 0.6650 (mtp180) REVERT: H 88 GLU cc_start: 0.9031 (pp20) cc_final: 0.8608 (pp20) REVERT: H 89 ASP cc_start: 0.8185 (m-30) cc_final: 0.7913 (m-30) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 1.2578 time to fit residues: 93.7584 Evaluate side-chains 74 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 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 = 0.3407 r_free = 0.3407 target = 0.085529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073394 restraints weight = 5887.429| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.11 r_work: 0.3070 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2550 Z= 0.193 Angle : 0.626 7.976 3469 Z= 0.305 Chirality : 0.044 0.136 370 Planarity : 0.004 0.037 448 Dihedral : 4.998 42.001 373 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.87 % Allowed : 24.72 % Favored : 70.41 % 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: -1.15 (0.44), residues: 310 helix: -2.82 (1.20), residues: 20 sheet: -0.45 (0.45), residues: 110 loop : -0.64 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE C 392 TYR 0.013 0.001 TYR H 101 ARG 0.009 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8685 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: C 420 ASP cc_start: 0.8536 (m-30) cc_final: 0.8143 (m-30) REVERT: C 424 LYS cc_start: 0.9004 (tptt) cc_final: 0.8686 (tppp) REVERT: C 444 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8151 (mtmm) REVERT: C 516 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6731 (tm-30) REVERT: H 39 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: H 74 SER cc_start: 0.9232 (m) cc_final: 0.8988 (t) REVERT: H 86 ARG cc_start: 0.7287 (mtp180) cc_final: 0.6643 (mtp180) REVERT: H 88 GLU cc_start: 0.9047 (pp20) cc_final: 0.8628 (pp20) REVERT: H 89 ASP cc_start: 0.8159 (m-30) cc_final: 0.7906 (m-30) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 1.2425 time to fit residues: 91.3911 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.086275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073800 restraints weight = 5967.321| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.26 r_work: 0.3055 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2550 Z= 0.232 Angle : 0.663 8.053 3469 Z= 0.326 Chirality : 0.045 0.147 370 Planarity : 0.004 0.042 448 Dihedral : 5.032 42.147 373 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.24 % Allowed : 24.72 % Favored : 70.04 % 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: -1.12 (0.44), residues: 310 helix: -2.76 (1.22), residues: 20 sheet: -0.43 (0.46), residues: 104 loop : -0.62 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.006 0.001 PHE C 347 TYR 0.009 0.001 TYR C 495 ARG 0.009 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8493 (m-30) cc_final: 0.8076 (m-30) REVERT: C 424 LYS cc_start: 0.8996 (tptt) cc_final: 0.8649 (tppp) REVERT: C 444 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8138 (mtmm) REVERT: C 516 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6866 (tm-30) REVERT: H 39 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: H 74 SER cc_start: 0.9230 (m) cc_final: 0.8999 (t) REVERT: H 86 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6657 (mtp180) REVERT: H 88 GLU cc_start: 0.9075 (pp20) cc_final: 0.8646 (pp20) REVERT: H 89 ASP cc_start: 0.8192 (m-30) cc_final: 0.7937 (m-30) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 1.2173 time to fit residues: 88.3105 Evaluate side-chains 73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 23 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.3438 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.087798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075313 restraints weight = 5889.035| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.21 r_work: 0.3085 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2550 Z= 0.167 Angle : 0.643 8.351 3469 Z= 0.314 Chirality : 0.044 0.134 370 Planarity : 0.004 0.037 448 Dihedral : 4.628 36.905 373 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.87 % Allowed : 25.84 % Favored : 69.29 % 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: -1.00 (0.44), residues: 310 helix: -2.79 (1.20), residues: 20 sheet: -0.26 (0.47), residues: 100 loop : -0.59 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.005 0.001 PHE C 347 TYR 0.013 0.001 TYR H 101 ARG 0.008 0.001 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8705 (ptm-80) cc_final: 0.8492 (ptm-80) REVERT: C 420 ASP cc_start: 0.8482 (m-30) cc_final: 0.8074 (m-30) REVERT: C 424 LYS cc_start: 0.9009 (tptt) cc_final: 0.8660 (tppp) REVERT: C 444 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8167 (mtmm) REVERT: C 516 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7025 (tm-30) REVERT: C 517 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7100 (mm) REVERT: H 39 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: H 74 SER cc_start: 0.9171 (m) cc_final: 0.8958 (t) REVERT: H 86 ARG cc_start: 0.7261 (mtp180) cc_final: 0.6597 (mtp180) REVERT: H 88 GLU cc_start: 0.9059 (pp20) cc_final: 0.8786 (pp20) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 1.2178 time to fit residues: 90.8385 Evaluate side-chains 73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 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 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074339 restraints weight = 6020.290| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.27 r_work: 0.3049 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2550 Z= 0.223 Angle : 0.669 8.966 3469 Z= 0.325 Chirality : 0.045 0.137 370 Planarity : 0.004 0.040 448 Dihedral : 4.799 39.897 373 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.87 % Allowed : 25.47 % Favored : 69.66 % 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: -0.98 (0.44), residues: 310 helix: -2.68 (1.24), residues: 20 sheet: -0.09 (0.51), residues: 90 loop : -0.67 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.006 0.001 PHE C 347 TYR 0.009 0.001 TYR C 495 ARG 0.010 0.001 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.90 seconds wall clock time: 46 minutes 46.47 seconds (2806.47 seconds total)