Starting phenix.real_space_refine on Tue Feb 11 00:57:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsc_32753/02_2025/7wsc_32753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsc_32753/02_2025/7wsc_32753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsc_32753/02_2025/7wsc_32753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsc_32753/02_2025/7wsc_32753.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsc_32753/02_2025/7wsc_32753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsc_32753/02_2025/7wsc_32753.cif" } resolution = 3.78 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= 0.019 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 15 5.16 5 C 2156 2.51 5 N 563 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3369 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.35, per 1000 atoms: 0.99 Number of scatterers: 3369 At special positions: 0 Unit cell: (63.13, 87.74, 74.9, 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 15 16.00 O 635 8.00 N 563 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.01 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 410.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 338 through 344 Processing helix chain 'R' and resid 364 through 369 removed outlier: 3.593A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 388 removed outlier: 4.117A pdb=" N ASN R 388 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.870A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O VAL H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'L' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.915A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 397 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.861A pdb=" N LEU H 37 " --> pdb=" O MET H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 65 through 70 removed outlier: 6.433A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 144 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.736A pdb=" N THR L 24 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.554A pdb=" N ILE L 109 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 183 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: 0.73 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 532 1.26 - 1.40: 979 1.40 - 1.54: 1912 1.54 - 1.68: 17 1.68 - 1.82: 18 Bond restraints: 3458 Sorted by residual: bond pdb=" CA TYR R 380 " pdb=" C TYR R 380 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.35e-02 5.49e+03 9.08e+01 bond pdb=" C PHE R 377 " pdb=" O PHE R 377 " ideal model delta sigma weight residual 1.235 1.116 0.120 1.26e-02 6.30e+03 9.01e+01 bond pdb=" C VAL R 382 " pdb=" O VAL R 382 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.03e-02 9.43e+03 6.47e+01 bond pdb=" CB TYR R 380 " pdb=" CG TYR R 380 " ideal model delta sigma weight residual 1.512 1.341 0.171 2.20e-02 2.07e+03 6.07e+01 bond pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 1.523 1.436 0.088 1.25e-02 6.40e+03 4.91e+01 ... (remaining 3453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 4634 6.03 - 12.06: 48 12.06 - 18.09: 10 18.09 - 24.12: 1 24.12 - 30.15: 2 Bond angle restraints: 4695 Sorted by residual: angle pdb=" N GLY R 482 " pdb=" CA GLY R 482 " pdb=" C GLY R 482 " ideal model delta sigma weight residual 113.18 85.51 27.67 2.37e+00 1.78e-01 1.36e+02 angle pdb=" C PHE R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.84 132.96 -13.12 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N PHE R 486 " pdb=" CA PHE R 486 " pdb=" C PHE R 486 " ideal model delta sigma weight residual 111.04 95.20 15.84 1.55e+00 4.16e-01 1.04e+02 angle pdb=" N ALA R 475 " pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 107.98 89.55 18.43 1.88e+00 2.83e-01 9.61e+01 angle pdb=" CA PRO L 37 " pdb=" N PRO L 37 " pdb=" CD PRO L 37 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 ... (remaining 4690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1778 15.87 - 31.73: 183 31.73 - 47.60: 60 47.60 - 63.46: 15 63.46 - 79.32: 8 Dihedral angle restraints: 2044 sinusoidal: 827 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.68 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" N CYS R 488 " pdb=" C CYS R 488 " pdb=" CA CYS R 488 " pdb=" CB CYS R 488 " ideal model delta harmonic sigma weight residual 122.80 106.51 16.29 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ARG H 71 " pdb=" C ARG H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 2041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 476 0.158 - 0.317: 11 0.317 - 0.475: 6 0.475 - 0.633: 4 0.633 - 0.791: 2 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA CYS R 379 " pdb=" N CYS R 379 " pdb=" C CYS R 379 " pdb=" CB CYS R 379 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN R 477 " pdb=" N ASN R 477 " pdb=" C ASN R 477 " pdb=" CB ASN R 477 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 496 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.119 5.00e-02 4.00e+02 1.69e-01 4.60e+01 pdb=" N PRO R 491 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 368 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU R 368 " 0.111 2.00e-02 2.50e+03 pdb=" O LEU R 368 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR R 369 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 477 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASN R 477 " -0.110 2.00e-02 2.50e+03 pdb=" O ASN R 477 " 0.043 2.00e-02 2.50e+03 pdb=" N LYS R 478 " 0.035 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 9 2.26 - 2.92: 1670 2.92 - 3.58: 4936 3.58 - 4.24: 7946 4.24 - 4.90: 13267 Nonbonded interactions: 27828 Sorted by model distance: nonbonded pdb=" O TYR R 473 " pdb=" O CYS R 488 " model vdw 1.600 3.040 nonbonded pdb=" OG1 THR L 33 " pdb=" OE2 GLU L 36 " model vdw 2.071 3.040 nonbonded pdb=" O ASN R 477 " pdb=" ND2 ASN R 477 " model vdw 2.084 3.120 nonbonded pdb=" OG SER H 36 " pdb=" O MET H 102 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.118 3.040 ... (remaining 27823 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 group one per residue 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.370 Find NCS groups from input model: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.013 0.171 3458 Z= 0.821 Angle : 1.667 30.153 4695 Z= 0.880 Chirality : 0.101 0.791 499 Planarity : 0.012 0.169 604 Dihedral : 15.341 79.299 1263 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 41.09 Ramachandran Plot: Outliers : 3.62 % Allowed : 14.73 % Favored : 81.64 % Rotamer: Outliers : 4.99 % Allowed : 1.94 % Favored : 93.07 % Cbeta Deviations : 1.31 % Peptide Plane: Cis-proline : 10.00 % 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: -4.09 (0.39), residues: 414 helix: -5.03 (0.30), residues: 12 sheet: -2.57 (0.41), residues: 129 loop : -2.82 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 59 HIS 0.015 0.005 HIS H 54 PHE 0.056 0.004 PHE R 490 TYR 0.023 0.002 TYR H 51 ARG 0.039 0.002 ARG R 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.598 Fit side-chains REVERT: R 377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: R 423 TYR cc_start: 0.7992 (t80) cc_final: 0.7695 (t80) REVERT: R 455 LEU cc_start: 0.7505 (pt) cc_final: 0.7293 (pt) REVERT: R 486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6242 (t80) REVERT: L 32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7557 (p) REVERT: L 50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7213 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7826 (m-80) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.1619 time to fit residues: 25.6333 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 474 GLN Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 486 PHE Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain L residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 474 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 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 = 0.3843 r_free = 0.3843 target = 0.139927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115314 restraints weight = 5825.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119290 restraints weight = 3388.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122093 restraints weight = 2335.573| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 3458 Z= 0.423 Angle : 0.991 13.883 4695 Z= 0.492 Chirality : 0.056 0.373 499 Planarity : 0.010 0.149 604 Dihedral : 10.162 86.175 542 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.80 % Favored : 86.47 % Rotamer: Outliers : 6.37 % Allowed : 14.40 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.66 (0.39), residues: 414 helix: -3.30 (1.06), residues: 12 sheet: -2.49 (0.40), residues: 128 loop : -2.46 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 59 HIS 0.009 0.003 HIS H 54 PHE 0.025 0.003 PHE R 486 TYR 0.023 0.002 TYR H 51 ARG 0.009 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 374 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6055 (p90) REVERT: R 377 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: R 423 TYR cc_start: 0.8189 (t80) cc_final: 0.7877 (t80) REVERT: R 472 ILE cc_start: 0.3324 (OUTLIER) cc_final: 0.3090 (mm) REVERT: L 26 SER cc_start: 0.6961 (OUTLIER) cc_final: 0.6670 (p) REVERT: L 28 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7214 (tt) REVERT: L 50 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7278 (tm-30) REVERT: L 111 TYR cc_start: 0.8453 (m-80) cc_final: 0.7703 (m-80) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 0.1386 time to fit residues: 19.7136 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 358 ILE Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 488 CYS Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116954 restraints weight = 5694.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121023 restraints weight = 3323.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123861 restraints weight = 2299.087| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 3458 Z= 0.311 Angle : 0.862 13.660 4695 Z= 0.431 Chirality : 0.050 0.179 499 Planarity : 0.008 0.139 604 Dihedral : 8.350 58.804 534 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 6.65 % Allowed : 17.73 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.32 (0.41), residues: 414 helix: -3.36 (0.98), residues: 12 sheet: -2.50 (0.41), residues: 130 loop : -2.06 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 59 HIS 0.005 0.002 HIS H 54 PHE 0.014 0.002 PHE R 375 TYR 0.019 0.002 TYR H 51 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: R 423 TYR cc_start: 0.8117 (t80) cc_final: 0.7808 (t80) REVERT: R 452 LEU cc_start: 0.8209 (mt) cc_final: 0.7983 (mt) REVERT: H 72 TYR cc_start: 0.7113 (p90) cc_final: 0.6653 (p90) REVERT: L 28 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7209 (tt) REVERT: L 42 CYS cc_start: 0.6195 (m) cc_final: 0.5914 (m) REVERT: L 50 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7325 (tm-30) REVERT: L 52 ASN cc_start: 0.8556 (p0) cc_final: 0.8063 (p0) REVERT: L 62 GLN cc_start: 0.8741 (pt0) cc_final: 0.8508 (pt0) REVERT: L 74 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8474 (tt) REVERT: L 111 TYR cc_start: 0.8264 (m-80) cc_final: 0.7669 (m-80) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.1405 time to fit residues: 21.3552 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 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 = 0.3877 r_free = 0.3877 target = 0.142078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117629 restraints weight = 5792.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121820 restraints weight = 3276.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124725 restraints weight = 2228.112| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 3458 Z= 0.332 Angle : 0.830 13.789 4695 Z= 0.414 Chirality : 0.049 0.169 499 Planarity : 0.007 0.133 604 Dihedral : 7.791 54.238 527 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.59 % Favored : 87.92 % Rotamer: Outliers : 6.93 % Allowed : 19.67 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.16 (0.41), residues: 414 helix: -3.40 (0.94), residues: 12 sheet: -2.48 (0.41), residues: 130 loop : -1.88 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.012 0.002 PHE H 48 TYR 0.011 0.002 TYR H 51 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8177 (t80) cc_final: 0.7863 (t80) REVERT: R 489 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.7037 (t80) REVERT: H 25 GLU cc_start: 0.7005 (pm20) cc_final: 0.6717 (pm20) REVERT: H 71 ARG cc_start: 0.7683 (mtt90) cc_final: 0.7336 (mtt90) REVERT: H 72 TYR cc_start: 0.7182 (p90) cc_final: 0.6610 (p90) REVERT: L 62 GLN cc_start: 0.8655 (pt0) cc_final: 0.7999 (pt0) REVERT: L 74 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8461 (tt) REVERT: L 111 TYR cc_start: 0.8308 (m-80) cc_final: 0.7634 (m-80) outliers start: 25 outliers final: 19 residues processed: 116 average time/residue: 0.1406 time to fit residues: 20.1395 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 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 = 0.3881 r_free = 0.3881 target = 0.142092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117940 restraints weight = 5780.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122155 restraints weight = 3298.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125092 restraints weight = 2235.296| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 3458 Z= 0.307 Angle : 0.836 13.728 4695 Z= 0.413 Chirality : 0.048 0.167 499 Planarity : 0.007 0.128 604 Dihedral : 7.284 50.517 525 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.39 % Favored : 89.13 % Rotamer: Outliers : 8.59 % Allowed : 21.33 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.99 (0.41), residues: 414 helix: -3.27 (1.00), residues: 12 sheet: -2.37 (0.42), residues: 131 loop : -1.75 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 59 HIS 0.001 0.001 HIS H 54 PHE 0.013 0.002 PHE H 133 TYR 0.021 0.002 TYR L 56 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8143 (t80) cc_final: 0.7849 (t80) REVERT: R 489 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6900 (t80) REVERT: H 32 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6418 (mm-40) REVERT: H 71 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7519 (mtt90) REVERT: H 72 TYR cc_start: 0.7179 (p90) cc_final: 0.6621 (p90) REVERT: H 123 TYR cc_start: 0.8707 (p90) cc_final: 0.8369 (p90) REVERT: L 50 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7523 (tm-30) REVERT: L 62 GLN cc_start: 0.8624 (pt0) cc_final: 0.8019 (pt0) REVERT: L 74 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8487 (tt) REVERT: L 111 TYR cc_start: 0.8193 (m-80) cc_final: 0.7700 (m-80) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 0.1577 time to fit residues: 22.3970 Evaluate side-chains 121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN ** L 62 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 = 0.3931 r_free = 0.3931 target = 0.146059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122340 restraints weight = 5892.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126458 restraints weight = 3441.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129359 restraints weight = 2354.016| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 3458 Z= 0.257 Angle : 0.813 13.663 4695 Z= 0.400 Chirality : 0.047 0.153 499 Planarity : 0.007 0.124 604 Dihedral : 6.990 47.794 525 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.14 % Favored : 89.37 % Rotamer: Outliers : 7.20 % Allowed : 24.10 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.87 (0.41), residues: 414 helix: -3.59 (0.75), residues: 18 sheet: -2.13 (0.44), residues: 124 loop : -1.70 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 59 HIS 0.000 0.000 HIS R 505 PHE 0.014 0.002 PHE L 122 TYR 0.018 0.001 TYR L 73 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8113 (t80) cc_final: 0.7788 (t80) REVERT: R 489 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.7069 (t80) REVERT: H 32 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6586 (mm-40) REVERT: H 71 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7496 (mtt90) REVERT: H 72 TYR cc_start: 0.7176 (p90) cc_final: 0.6632 (p90) REVERT: H 123 TYR cc_start: 0.8633 (p90) cc_final: 0.8348 (p90) REVERT: L 50 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7633 (tm-30) REVERT: L 62 GLN cc_start: 0.8550 (pt0) cc_final: 0.7971 (pt0) REVERT: L 74 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8427 (tt) REVERT: L 111 TYR cc_start: 0.8093 (m-80) cc_final: 0.7707 (m-80) outliers start: 26 outliers final: 18 residues processed: 119 average time/residue: 0.1513 time to fit residues: 21.9869 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120283 restraints weight = 5809.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124576 restraints weight = 3293.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.127521 restraints weight = 2222.894| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3458 Z= 0.263 Angle : 0.806 13.799 4695 Z= 0.397 Chirality : 0.047 0.149 499 Planarity : 0.007 0.121 604 Dihedral : 6.852 47.264 525 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 7.20 % Allowed : 24.65 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.78 (0.41), residues: 414 helix: -3.56 (0.75), residues: 18 sheet: -2.02 (0.45), residues: 124 loop : -1.67 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 59 HIS 0.000 0.000 HIS R 505 PHE 0.013 0.002 PHE L 122 TYR 0.018 0.001 TYR L 73 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8173 (t80) cc_final: 0.7852 (t80) REVERT: R 489 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.7091 (t80) REVERT: H 32 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6666 (mm-40) REVERT: H 35 ARG cc_start: 0.7455 (ptt-90) cc_final: 0.7246 (ptt-90) REVERT: H 72 TYR cc_start: 0.7192 (p90) cc_final: 0.6602 (p90) REVERT: H 123 TYR cc_start: 0.8595 (p90) cc_final: 0.8339 (p90) REVERT: L 50 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7636 (tm-30) REVERT: L 62 GLN cc_start: 0.8537 (pt0) cc_final: 0.8078 (pt0) REVERT: L 74 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8445 (tt) REVERT: L 78 ARG cc_start: 0.8378 (ptp90) cc_final: 0.8175 (ptp-170) REVERT: L 111 TYR cc_start: 0.8227 (m-80) cc_final: 0.7786 (m-80) outliers start: 26 outliers final: 20 residues processed: 115 average time/residue: 0.1759 time to fit residues: 24.2301 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119510 restraints weight = 5840.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123700 restraints weight = 3318.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126668 restraints weight = 2256.397| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3458 Z= 0.280 Angle : 0.808 13.971 4695 Z= 0.398 Chirality : 0.047 0.147 499 Planarity : 0.007 0.118 604 Dihedral : 6.833 47.194 525 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 7.76 % Allowed : 25.21 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.75 (0.42), residues: 414 helix: -3.59 (0.73), residues: 18 sheet: -1.94 (0.45), residues: 124 loop : -1.68 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.011 0.002 PHE L 95 TYR 0.019 0.001 TYR L 73 ARG 0.007 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8185 (t80) cc_final: 0.7896 (t80) REVERT: R 489 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.7061 (t80) REVERT: H 32 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6720 (mm-40) REVERT: H 72 TYR cc_start: 0.7205 (p90) cc_final: 0.6727 (p90) REVERT: H 123 TYR cc_start: 0.8587 (p90) cc_final: 0.8344 (p90) REVERT: L 50 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7750 (tm-30) REVERT: L 62 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: L 74 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8522 (tt) REVERT: L 111 TYR cc_start: 0.8190 (m-80) cc_final: 0.7768 (m-80) outliers start: 28 outliers final: 22 residues processed: 114 average time/residue: 0.1546 time to fit residues: 21.3397 Evaluate side-chains 118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119904 restraints weight = 5695.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124047 restraints weight = 3272.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.126980 restraints weight = 2228.225| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3458 Z= 0.284 Angle : 0.808 13.785 4695 Z= 0.401 Chirality : 0.047 0.166 499 Planarity : 0.007 0.116 604 Dihedral : 6.902 47.099 525 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 7.48 % Allowed : 26.04 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.73 (0.42), residues: 414 helix: -3.60 (0.73), residues: 18 sheet: -1.92 (0.46), residues: 124 loop : -1.67 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.012 0.002 PHE L 95 TYR 0.020 0.001 TYR L 73 ARG 0.011 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8202 (t80) cc_final: 0.7962 (t80) REVERT: R 489 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.7197 (t80) REVERT: H 32 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6723 (mm-40) REVERT: L 62 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: L 74 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8544 (tt) REVERT: L 85 ARG cc_start: 0.8694 (ptt-90) cc_final: 0.8268 (ptt180) REVERT: L 111 TYR cc_start: 0.8203 (m-80) cc_final: 0.7746 (m-80) outliers start: 27 outliers final: 20 residues processed: 107 average time/residue: 0.1664 time to fit residues: 21.3222 Evaluate side-chains 112 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4488 > 50: distance: 75 - 200: 18.340 distance: 107 - 204: 18.025 distance: 110 - 201: 22.476 distance: 126 - 186: 25.616 distance: 129 - 183: 32.733 distance: 165 - 171: 26.616 distance: 171 - 172: 5.037 distance: 172 - 173: 10.107 distance: 172 - 175: 25.332 distance: 173 - 174: 3.832 distance: 173 - 183: 5.750 distance: 175 - 176: 39.792 distance: 176 - 177: 7.240 distance: 176 - 178: 22.637 distance: 177 - 179: 12.613 distance: 178 - 180: 9.491 distance: 179 - 181: 18.048 distance: 180 - 181: 15.054 distance: 181 - 182: 18.001 distance: 183 - 184: 30.886 distance: 184 - 185: 11.697 distance: 184 - 187: 7.354 distance: 185 - 186: 11.140 distance: 185 - 195: 24.705 distance: 187 - 188: 15.458 distance: 188 - 189: 12.077 distance: 188 - 190: 9.406 distance: 189 - 191: 7.327 distance: 190 - 192: 19.580 distance: 191 - 193: 19.376 distance: 192 - 193: 19.552 distance: 193 - 194: 14.977 distance: 195 - 196: 20.727 distance: 196 - 197: 9.244 distance: 196 - 199: 11.129 distance: 197 - 198: 12.162 distance: 197 - 201: 11.748 distance: 199 - 200: 22.693 distance: 201 - 202: 15.481 distance: 202 - 203: 7.558 distance: 202 - 205: 9.183 distance: 203 - 204: 8.175 distance: 203 - 209: 10.052 distance: 205 - 206: 27.577 distance: 206 - 207: 15.704 distance: 207 - 208: 29.558 distance: 209 - 210: 9.020 distance: 210 - 211: 8.955 distance: 210 - 213: 9.430 distance: 211 - 212: 11.435 distance: 211 - 218: 8.405 distance: 213 - 214: 4.316 distance: 214 - 215: 15.697 distance: 215 - 216: 13.533 distance: 215 - 217: 8.412 distance: 218 - 219: 6.072 distance: 219 - 220: 9.844 distance: 219 - 222: 21.090 distance: 220 - 221: 14.055 distance: 220 - 223: 9.041 distance: 223 - 224: 10.625 distance: 224 - 225: 7.214 distance: 224 - 227: 7.908 distance: 225 - 226: 20.352 distance: 225 - 231: 7.357 distance: 227 - 228: 6.612 distance: 228 - 229: 17.142 distance: 228 - 230: 32.678 distance: 231 - 232: 15.252 distance: 232 - 233: 4.194 distance: 232 - 235: 12.267 distance: 233 - 234: 4.537 distance: 233 - 240: 4.081 distance: 235 - 236: 10.810 distance: 236 - 237: 11.165 distance: 237 - 238: 6.234 distance: 237 - 239: 10.346 distance: 240 - 241: 3.982 distance: 241 - 242: 11.680 distance: 241 - 244: 20.411 distance: 242 - 243: 11.918 distance: 242 - 247: 9.450 distance: 244 - 245: 11.295 distance: 244 - 246: 6.270 distance: 247 - 248: 6.906 distance: 247 - 253: 5.324 distance: 248 - 249: 13.895 distance: 248 - 251: 7.809 distance: 249 - 250: 10.026 distance: 249 - 254: 9.268 distance: 251 - 252: 7.070 distance: 252 - 253: 12.293