Starting phenix.real_space_refine on Fri Aug 22 13:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsc_32753/08_2025/7wsc_32753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsc_32753/08_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_32753/08_2025/7wsc_32753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsc_32753/08_2025/7wsc_32753.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsc_32753/08_2025/7wsc_32753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsc_32753/08_2025/7wsc_32753.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.90, per 1000 atoms: 0.27 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: 0.28 Conformation dependent library (CDL) restraints added in 94.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.08 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: 0.31 Time building geometry restraints manager: 0.37 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: 2.680 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.700 ------------------------------------------------------------------------------- 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 3465 Z= 0.744 Angle : 1.675 30.153 4711 Z= 0.883 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.039 0.002 ARG R 493 TYR 0.023 0.002 TYR H 51 PHE 0.056 0.004 PHE R 490 TRP 0.031 0.003 TRP L 59 HIS 0.015 0.005 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.01274 ( 3458) covalent geometry : angle 1.66708 ( 4695) SS BOND : bond 0.01209 ( 5) SS BOND : angle 4.15259 ( 10) hydrogen bonds : bond 0.26234 ( 74) hydrogen bonds : angle 12.54557 ( 183) link_BETA1-4 : bond 0.00848 ( 1) link_BETA1-4 : angle 0.61650 ( 3) link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 0.76176 ( 3) *********************** 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 : 0.080 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: 0.7291 (pt) REVERT: R 486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6241 (t80) REVERT: L 32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7558 (p) REVERT: L 50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7214 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7828 (m-80) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.0590 time to fit residues: 9.4599 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 : 0.084 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 474 GLN R 477 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.144627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120087 restraints weight = 5799.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124291 restraints weight = 3329.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127252 restraints weight = 2267.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129255 restraints weight = 1718.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130656 restraints weight = 1401.649| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 3465 Z= 0.197 Angle : 0.984 13.415 4711 Z= 0.488 Chirality : 0.055 0.363 499 Planarity : 0.010 0.146 604 Dihedral : 10.090 87.953 542 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.32 % Favored : 86.96 % Rotamer: Outliers : 6.37 % Allowed : 13.02 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.64 (0.40), residues: 414 helix: -3.13 (1.15), residues: 12 sheet: -2.53 (0.40), residues: 132 loop : -2.41 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 91 TYR 0.024 0.002 TYR H 51 PHE 0.018 0.002 PHE R 375 TRP 0.016 0.002 TRP L 59 HIS 0.008 0.003 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 3458) covalent geometry : angle 0.97981 ( 4695) SS BOND : bond 0.00547 ( 5) SS BOND : angle 2.19436 ( 10) hydrogen bonds : bond 0.04910 ( 74) hydrogen bonds : angle 8.99390 ( 183) link_BETA1-4 : bond 0.00576 ( 1) link_BETA1-4 : angle 1.02188 ( 3) link_NAG-ASN : bond 0.00292 ( 1) link_NAG-ASN : angle 0.77135 ( 3) *********************** 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 129 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: R 374 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5876 (p90) REVERT: R 377 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: R 423 TYR cc_start: 0.8048 (t80) cc_final: 0.7679 (t80) REVERT: R 441 LEU cc_start: 0.7230 (tt) cc_final: 0.6925 (mt) REVERT: R 472 ILE cc_start: 0.3356 (OUTLIER) cc_final: 0.3130 (mm) REVERT: R 486 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6563 (t80) REVERT: H 134 TYR cc_start: 0.8609 (p90) cc_final: 0.8003 (p90) REVERT: L 50 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7410 (tm-30) REVERT: L 111 TYR cc_start: 0.8417 (m-80) cc_final: 0.7630 (m-80) outliers start: 23 outliers final: 14 residues processed: 119 average time/residue: 0.0496 time to fit residues: 7.4053 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 486 PHE Chi-restraints excluded: chain R residue 488 CYS 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 89 ILE Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119330 restraints weight = 5813.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123553 restraints weight = 3336.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126521 restraints weight = 2280.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128491 restraints weight = 1727.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129952 restraints weight = 1417.693| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 3465 Z= 0.191 Angle : 0.860 14.044 4711 Z= 0.434 Chirality : 0.050 0.182 499 Planarity : 0.008 0.137 604 Dihedral : 8.160 59.649 532 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.59 % Favored : 87.68 % Rotamer: Outliers : 4.99 % Allowed : 18.01 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.40), residues: 414 helix: -3.20 (1.03), residues: 12 sheet: -2.46 (0.40), residues: 129 loop : -2.05 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 91 TYR 0.017 0.002 TYR H 51 PHE 0.015 0.002 PHE R 375 TRP 0.015 0.002 TRP L 59 HIS 0.005 0.002 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 3458) covalent geometry : angle 0.85607 ( 4695) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.90783 ( 10) hydrogen bonds : bond 0.03969 ( 74) hydrogen bonds : angle 8.34257 ( 183) link_BETA1-4 : bond 0.00197 ( 1) link_BETA1-4 : angle 0.85526 ( 3) link_NAG-ASN : bond 0.00032 ( 1) link_NAG-ASN : angle 1.08010 ( 3) *********************** 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 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: R 423 TYR cc_start: 0.8016 (t80) cc_final: 0.7617 (t80) REVERT: H 134 TYR cc_start: 0.8725 (p90) cc_final: 0.8230 (p90) REVERT: L 28 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7154 (tt) REVERT: L 50 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7304 (tm-30) REVERT: L 52 ASN cc_start: 0.8514 (p0) cc_final: 0.8089 (p0) REVERT: L 74 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8392 (tt) REVERT: L 111 TYR cc_start: 0.8242 (m-80) cc_final: 0.7704 (m-80) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.0691 time to fit residues: 9.8545 Evaluate side-chains 110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 89 ILE 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 24 THR 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 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.0050 chunk 13 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123601 restraints weight = 5687.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127941 restraints weight = 3211.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130937 restraints weight = 2159.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132801 restraints weight = 1613.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134303 restraints weight = 1313.730| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 3465 Z= 0.141 Angle : 0.802 13.567 4711 Z= 0.396 Chirality : 0.048 0.161 499 Planarity : 0.007 0.132 604 Dihedral : 7.544 55.548 527 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.86 % Rotamer: Outliers : 5.26 % Allowed : 21.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.41), residues: 414 helix: -3.47 (0.82), residues: 18 sheet: -2.39 (0.41), residues: 132 loop : -1.84 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 91 TYR 0.019 0.001 TYR H 51 PHE 0.013 0.002 PHE R 375 TRP 0.019 0.002 TRP L 59 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3458) covalent geometry : angle 0.79955 ( 4695) SS BOND : bond 0.00262 ( 5) SS BOND : angle 1.50290 ( 10) hydrogen bonds : bond 0.03645 ( 74) hydrogen bonds : angle 7.64414 ( 183) link_BETA1-4 : bond 0.00457 ( 1) link_BETA1-4 : angle 0.89937 ( 3) link_NAG-ASN : bond 0.00148 ( 1) link_NAG-ASN : angle 0.98080 ( 3) *********************** 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 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: R 423 TYR cc_start: 0.7833 (t80) cc_final: 0.7497 (t80) REVERT: R 489 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6959 (t80) REVERT: H 32 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.5970 (mm-40) REVERT: H 134 TYR cc_start: 0.8652 (p90) cc_final: 0.8003 (p90) REVERT: L 62 GLN cc_start: 0.8597 (pt0) cc_final: 0.8365 (pt0) REVERT: L 74 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8353 (tt) REVERT: L 111 TYR cc_start: 0.8211 (m-80) cc_final: 0.7672 (m-80) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.0659 time to fit residues: 9.6093 Evaluate side-chains 109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 32 GLN Chi-restraints excluded: chain H residue 98 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN H 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121765 restraints weight = 5747.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126083 restraints weight = 3247.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129063 restraints weight = 2174.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131102 restraints weight = 1628.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132605 restraints weight = 1310.605| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 3465 Z= 0.165 Angle : 0.796 13.706 4711 Z= 0.393 Chirality : 0.047 0.157 499 Planarity : 0.007 0.128 604 Dihedral : 7.392 52.705 527 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.14 % Favored : 89.37 % Rotamer: Outliers : 6.93 % Allowed : 21.33 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.41), residues: 414 helix: -3.51 (0.79), residues: 18 sheet: -2.16 (0.41), residues: 138 loop : -1.71 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 101 TYR 0.016 0.001 TYR L 56 PHE 0.014 0.002 PHE H 133 TRP 0.018 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3458) covalent geometry : angle 0.79256 ( 4695) SS BOND : bond 0.00257 ( 5) SS BOND : angle 1.78754 ( 10) hydrogen bonds : bond 0.03574 ( 74) hydrogen bonds : angle 7.49835 ( 183) link_BETA1-4 : bond 0.00429 ( 1) link_BETA1-4 : angle 0.97056 ( 3) link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.03548 ( 3) *********************** 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 131 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: R 423 TYR cc_start: 0.7807 (t80) cc_final: 0.7449 (t80) REVERT: R 489 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6866 (t80) REVERT: H 32 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5720 (mm-40) REVERT: H 72 TYR cc_start: 0.7046 (p90) cc_final: 0.6512 (p90) REVERT: L 50 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7519 (tm-30) REVERT: L 62 GLN cc_start: 0.8547 (pt0) cc_final: 0.7883 (pt0) REVERT: L 74 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8390 (tt) REVERT: L 106 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6549 (t0) REVERT: L 111 TYR cc_start: 0.8199 (m-80) cc_final: 0.7695 (m-80) outliers start: 25 outliers final: 19 residues processed: 119 average time/residue: 0.0753 time to fit residues: 10.8441 Evaluate side-chains 122 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 418 ILE 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 32 GLN 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 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 Chi-restraints excluded: chain L residue 106 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.142958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118828 restraints weight = 5742.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123080 restraints weight = 3262.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125993 restraints weight = 2209.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128004 restraints weight = 1670.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129320 restraints weight = 1356.005| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3465 Z= 0.204 Angle : 0.807 14.092 4711 Z= 0.399 Chirality : 0.047 0.154 499 Planarity : 0.007 0.125 604 Dihedral : 7.403 51.079 527 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.39 % Favored : 89.13 % Rotamer: Outliers : 8.59 % Allowed : 21.05 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.41), residues: 414 helix: -3.67 (0.72), residues: 18 sheet: -2.21 (0.42), residues: 139 loop : -1.70 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 91 TYR 0.016 0.001 TYR H 137 PHE 0.011 0.002 PHE H 48 TRP 0.021 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 3458) covalent geometry : angle 0.80326 ( 4695) SS BOND : bond 0.00287 ( 5) SS BOND : angle 1.74562 ( 10) hydrogen bonds : bond 0.03493 ( 74) hydrogen bonds : angle 7.50686 ( 183) link_BETA1-4 : bond 0.00322 ( 1) link_BETA1-4 : angle 0.98593 ( 3) link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.05000 ( 3) *********************** 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 133 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7985 (t80) cc_final: 0.7672 (t80) REVERT: R 489 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6969 (t80) REVERT: H 123 TYR cc_start: 0.8628 (p90) cc_final: 0.8311 (p90) REVERT: L 50 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7603 (tm-30) REVERT: L 62 GLN cc_start: 0.8539 (pt0) cc_final: 0.7920 (pt0) REVERT: L 73 TYR cc_start: 0.9042 (p90) cc_final: 0.8526 (p90) REVERT: L 74 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8487 (tt) REVERT: L 111 TYR cc_start: 0.8218 (m-80) cc_final: 0.7786 (m-80) outliers start: 31 outliers final: 25 residues processed: 119 average time/residue: 0.0691 time to fit residues: 9.9537 Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 418 ILE 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 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 89 ILE 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 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 33 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.0000 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 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 = 0.3898 r_free = 0.3898 target = 0.143058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118620 restraints weight = 5895.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122975 restraints weight = 3305.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125985 restraints weight = 2222.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127989 restraints weight = 1667.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129105 restraints weight = 1351.726| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3465 Z= 0.198 Angle : 0.819 14.061 4711 Z= 0.403 Chirality : 0.047 0.150 499 Planarity : 0.007 0.121 604 Dihedral : 7.360 50.425 527 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 7.48 % Allowed : 23.27 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.41), residues: 414 helix: -3.64 (0.71), residues: 18 sheet: -2.02 (0.45), residues: 123 loop : -1.84 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.014 0.001 TYR H 137 PHE 0.011 0.002 PHE H 87 TRP 0.026 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 3458) covalent geometry : angle 0.81628 ( 4695) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.67668 ( 10) hydrogen bonds : bond 0.03471 ( 74) hydrogen bonds : angle 7.47867 ( 183) link_BETA1-4 : bond 0.00395 ( 1) link_BETA1-4 : angle 1.01574 ( 3) link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 1.00845 ( 3) *********************** 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 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8008 (t80) cc_final: 0.7735 (t80) REVERT: R 489 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.7050 (t80) REVERT: L 25 GLN cc_start: 0.7250 (mt0) cc_final: 0.6817 (mt0) REVERT: L 50 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7689 (tm-30) REVERT: L 62 GLN cc_start: 0.8498 (pt0) cc_final: 0.7999 (pt0) REVERT: L 73 TYR cc_start: 0.9014 (p90) cc_final: 0.8488 (p90) REVERT: L 74 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8503 (tt) REVERT: L 111 TYR cc_start: 0.8239 (m-80) cc_final: 0.7695 (m-80) outliers start: 27 outliers final: 23 residues processed: 113 average time/residue: 0.0623 time to fit residues: 8.6268 Evaluate side-chains 118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 418 ILE 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 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 89 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.144672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120913 restraints weight = 5817.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125023 restraints weight = 3311.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127918 restraints weight = 2273.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129835 restraints weight = 1709.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131343 restraints weight = 1392.639| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3465 Z= 0.161 Angle : 0.801 14.116 4711 Z= 0.393 Chirality : 0.046 0.148 499 Planarity : 0.007 0.119 604 Dihedral : 6.846 48.090 525 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 8.03 % Allowed : 22.99 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.42), residues: 414 helix: -3.49 (0.77), residues: 18 sheet: -1.92 (0.46), residues: 123 loop : -1.74 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.014 0.001 TYR H 78 PHE 0.010 0.002 PHE H 87 TRP 0.029 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3458) covalent geometry : angle 0.79862 ( 4695) SS BOND : bond 0.00259 ( 5) SS BOND : angle 1.51120 ( 10) hydrogen bonds : bond 0.03441 ( 74) hydrogen bonds : angle 7.31041 ( 183) link_BETA1-4 : bond 0.00516 ( 1) link_BETA1-4 : angle 1.01063 ( 3) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 0.94582 ( 3) *********************** 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 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: R 423 TYR cc_start: 0.7995 (t80) cc_final: 0.7616 (t80) REVERT: R 489 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6978 (t80) REVERT: L 25 GLN cc_start: 0.7225 (mt0) cc_final: 0.6724 (mt0) REVERT: L 50 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7733 (tm-30) REVERT: L 62 GLN cc_start: 0.8497 (pt0) cc_final: 0.8067 (pt0) REVERT: L 73 TYR cc_start: 0.8966 (p90) cc_final: 0.8517 (p90) REVERT: L 74 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8543 (tt) REVERT: L 111 TYR cc_start: 0.8229 (m-80) cc_final: 0.7739 (m-80) outliers start: 29 outliers final: 21 residues processed: 110 average time/residue: 0.0562 time to fit residues: 7.5462 Evaluate side-chains 109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 418 ILE 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 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR 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 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 144 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 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 ** 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 = 0.3912 r_free = 0.3912 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120232 restraints weight = 5811.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124273 restraints weight = 3401.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127011 restraints weight = 2351.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129054 restraints weight = 1806.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130383 restraints weight = 1469.678| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3465 Z= 0.178 Angle : 0.817 14.117 4711 Z= 0.400 Chirality : 0.046 0.148 499 Planarity : 0.007 0.116 604 Dihedral : 6.850 47.933 525 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.08 % Favored : 87.44 % Rotamer: Outliers : 7.48 % Allowed : 24.10 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.42), residues: 414 helix: -3.56 (0.73), residues: 18 sheet: -1.80 (0.47), residues: 123 loop : -1.70 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 91 TYR 0.014 0.001 TYR H 123 PHE 0.011 0.002 PHE H 87 TRP 0.037 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 3458) covalent geometry : angle 0.81531 ( 4695) SS BOND : bond 0.00227 ( 5) SS BOND : angle 1.41879 ( 10) hydrogen bonds : bond 0.03402 ( 74) hydrogen bonds : angle 7.27321 ( 183) link_BETA1-4 : bond 0.00428 ( 1) link_BETA1-4 : angle 1.02607 ( 3) link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 0.96687 ( 3) *********************** 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 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.7986 (t80) cc_final: 0.7703 (t80) REVERT: R 489 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.7037 (t80) REVERT: L 25 GLN cc_start: 0.7272 (mt0) cc_final: 0.6839 (mt0) REVERT: L 62 GLN cc_start: 0.8553 (pt0) cc_final: 0.8144 (pt0) REVERT: L 73 TYR cc_start: 0.8983 (p90) cc_final: 0.8552 (p90) REVERT: L 74 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8598 (tt) REVERT: L 111 TYR cc_start: 0.8224 (m-80) cc_final: 0.7774 (m-80) outliers start: 27 outliers final: 23 residues processed: 110 average time/residue: 0.0559 time to fit residues: 7.5368 Evaluate side-chains 121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 418 ILE 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 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR 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 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 H residue 144 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8453 > 50: distance: 8 - 181: 6.442 distance: 11 - 178: 4.718 distance: 102 - 107: 9.869 distance: 107 - 108: 14.979 distance: 108 - 109: 32.010 distance: 108 - 111: 16.292 distance: 109 - 110: 3.770 distance: 109 - 115: 18.053 distance: 111 - 112: 21.462 distance: 111 - 113: 8.954 distance: 112 - 114: 7.391 distance: 115 - 116: 16.761 distance: 115 - 189: 8.516 distance: 116 - 117: 16.355 distance: 116 - 119: 15.481 distance: 117 - 118: 12.168 distance: 117 - 121: 12.495 distance: 118 - 186: 18.519 distance: 119 - 120: 17.006 distance: 121 - 122: 4.494 distance: 123 - 124: 5.911 distance: 125 - 126: 8.282 distance: 126 - 127: 7.161 distance: 127 - 128: 7.150 distance: 128 - 129: 7.844 distance: 129 - 130: 8.446 distance: 129 - 131: 10.724 distance: 132 - 133: 3.597 distance: 132 - 174: 10.905 distance: 133 - 134: 4.004 distance: 133 - 136: 7.828 distance: 134 - 135: 4.663 distance: 135 - 171: 4.961 distance: 136 - 137: 5.737 distance: 137 - 138: 5.981 distance: 137 - 139: 5.968 distance: 140 - 141: 4.031 distance: 141 - 142: 6.647 distance: 141 - 144: 5.578 distance: 142 - 143: 8.922 distance: 142 - 148: 11.394 distance: 144 - 145: 6.745 distance: 145 - 146: 5.567 distance: 145 - 147: 5.418 distance: 148 - 149: 8.228 distance: 149 - 150: 15.919 distance: 149 - 152: 11.567 distance: 150 - 151: 7.234 distance: 150 - 154: 6.136 distance: 152 - 153: 19.525 distance: 155 - 156: 9.233 distance: 155 - 158: 6.900 distance: 156 - 157: 5.485 distance: 156 - 163: 6.732 distance: 158 - 159: 11.527 distance: 159 - 160: 14.088 distance: 160 - 161: 10.285 distance: 161 - 162: 11.104 distance: 163 - 164: 7.719 distance: 164 - 165: 7.260 distance: 164 - 167: 11.562 distance: 165 - 171: 7.288 distance: 167 - 168: 10.029 distance: 168 - 169: 4.619 distance: 171 - 172: 3.576 distance: 172 - 175: 3.408 distance: 173 - 174: 3.384 distance: 175 - 176: 9.249 distance: 175 - 177: 5.808 distance: 178 - 179: 3.546 distance: 179 - 182: 3.124 distance: 180 - 186: 5.404 distance: 182 - 183: 5.132 distance: 183 - 184: 6.579 distance: 183 - 185: 5.734