Starting phenix.real_space_refine on Wed Jul 1 21:12:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.map" model { file = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2026/8dly_27520.cif" } resolution = 3.0 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= -0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1582 2.51 5 N 417 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2483 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.57, per 1000 atoms: 0.23 Number of scatterers: 2483 At special positions: 0 Unit cell: (68, 82, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 471 8.00 N 417 7.00 C 1582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 59.0 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.619A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.081A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.330A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.505A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.660A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.815A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.124A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 783 1.34 - 1.46: 649 1.46 - 1.58: 1102 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2550 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" CB ASN H 50 " pdb=" CG ASN H 50 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.19e-02 7.06e+03 2.32e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3270 1.92 - 3.84: 172 3.84 - 5.76: 21 5.76 - 7.68: 4 7.68 - 9.60: 2 Bond angle restraints: 3469 Sorted by residual: angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" C GLY C 476 " pdb=" N SER C 477 " pdb=" CA SER C 477 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.78e+00 angle pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta sigma weight residual 120.38 124.48 -4.10 1.37e+00 5.33e-01 8.95e+00 angle pdb=" N LEU C 518 " pdb=" CA LEU C 518 " pdb=" C LEU C 518 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 125.90 -9.60 3.50e+00 8.16e-02 7.52e+00 ... (remaining 3464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 1289 13.75 - 27.50: 144 27.50 - 41.25: 36 41.25 - 54.99: 9 54.99 - 68.74: 1 Dihedral angle restraints: 1479 sinusoidal: 572 harmonic: 907 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 126.09 -33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual 180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CG ARG C 509 " pdb=" CD ARG C 509 " pdb=" NE ARG C 509 " pdb=" CZ ARG C 509 " ideal model delta sinusoidal sigma weight residual -90.00 -131.99 41.99 2 1.50e+01 4.44e-03 9.55e+00 ... (remaining 1476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 224 0.046 - 0.093: 100 0.093 - 0.139: 38 0.139 - 0.185: 5 0.185 - 0.231: 3 Chirality restraints: 370 Sorted by residual: chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA MET H 106 " pdb=" N MET H 106 " pdb=" C MET H 106 " pdb=" CB MET H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 367 not shown) Planarity restraints: 449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 520 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA C 520 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 520 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO C 521 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN H 60 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO H 61 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 41 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.025 5.00e-02 4.00e+02 ... (remaining 446 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 789 2.83 - 3.35: 1927 3.35 - 3.87: 4036 3.87 - 4.38: 4493 4.38 - 4.90: 8057 Nonbonded interactions: 19302 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.317 3.040 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.432 3.120 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.487 3.120 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.505 3.040 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.524 3.040 ... (remaining 19297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.430 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 2556 Z= 0.237 Angle : 0.945 9.601 3482 Z= 0.513 Chirality : 0.059 0.231 370 Planarity : 0.006 0.053 448 Dihedral : 12.370 68.742 892 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.37 % Allowed : 3.00 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.40), residues: 310 helix: -3.94 (0.60), residues: 26 sheet: -0.08 (0.45), residues: 104 loop : -1.03 (0.37), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 97 TYR 0.015 0.002 TYR C 453 PHE 0.017 0.002 PHE H 27 TRP 0.021 0.003 TRP H 47 HIS 0.011 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 ( 2550) covalent geometry : angle 0.93943 / 0.51 ( 3469) SS BOND : bond 0.00516 / 0.27 ( 5) SS BOND : angle 1.21448 / 0.70 ( 10) hydrogen bonds : bond 0.13741 / 8.09 ( 74) hydrogen bonds : angle 9.45269 / 6.47 ( 186) link_NAG-ASN : bond 0.00546 / 0.29 ( 1) link_NAG-ASN : angle 3.46937 / 1.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.102 Fit side-chains REVERT: C 420 ASP cc_start: 0.8523 (m-30) cc_final: 0.8208 (m-30) REVERT: C 424 LYS cc_start: 0.8837 (tptt) cc_final: 0.8592 (tppp) REVERT: C 456 PHE cc_start: 0.8662 (t80) cc_final: 0.8216 (t80) REVERT: C 474 GLN cc_start: 0.7635 (mt0) cc_final: 0.7418 (mt0) REVERT: H 39 GLN cc_start: 0.7731 (pt0) cc_final: 0.7150 (pm20) REVERT: H 52 TYR cc_start: 0.8889 (m-80) cc_final: 0.8688 (m-80) REVERT: H 86 ARG cc_start: 0.6993 (mtp180) cc_final: 0.6617 (mtp180) REVERT: H 92 ILE cc_start: 0.8543 (mt) cc_final: 0.7761 (mm) outliers start: 1 outliers final: 2 residues processed: 100 average time/residue: 0.5023 time to fit residues: 51.3330 Evaluate side-chains 64 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 474 GLN C 506 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074686 restraints weight = 6008.559| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.19 r_work: 0.3074 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2556 Z= 0.181 Angle : 0.622 6.449 3482 Z= 0.313 Chirality : 0.045 0.147 370 Planarity : 0.005 0.032 448 Dihedral : 8.717 126.088 356 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.12 % Allowed : 16.85 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.42), residues: 310 helix: -3.44 (0.78), residues: 27 sheet: 0.04 (0.48), residues: 98 loop : -0.69 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 16 TYR 0.015 0.001 TYR H 79 PHE 0.008 0.001 PHE C 347 TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 2550) covalent geometry : angle 0.62049 / 0.31 ( 3469) SS BOND : bond 0.00446 / 0.23 ( 5) SS BOND : angle 0.72564 / 0.42 ( 10) hydrogen bonds : bond 0.03457 / 2.21 ( 74) hydrogen bonds : angle 7.34086 / 5.02 ( 186) link_NAG-ASN : bond 0.00337 / 0.18 ( 1) link_NAG-ASN : angle 1.52870 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8702 (m-30) cc_final: 0.8448 (m-30) REVERT: C 424 LYS cc_start: 0.8982 (tptt) cc_final: 0.8706 (tppp) REVERT: H 29 PHE cc_start: 0.8630 (t80) cc_final: 0.8203 (t80) REVERT: H 60 ASN cc_start: 0.9066 (t0) cc_final: 0.8836 (t0) REVERT: H 86 ARG cc_start: 0.7445 (mtp180) cc_final: 0.6657 (mtp180) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.5036 time to fit residues: 39.5647 Evaluate side-chains 68 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071886 restraints weight = 6075.483| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.14 r_work: 0.3019 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2556 Z= 0.178 Angle : 0.596 6.388 3482 Z= 0.302 Chirality : 0.045 0.138 370 Planarity : 0.004 0.031 448 Dihedral : 5.467 47.703 354 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.99 % Allowed : 17.98 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.43), residues: 310 helix: -3.32 (1.13), residues: 20 sheet: -0.11 (0.47), residues: 103 loop : -0.80 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 16 TYR 0.011 0.001 TYR H 79 PHE 0.013 0.001 PHE H 29 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 2550) covalent geometry : angle 0.59454 / 0.30 ( 3469) SS BOND : bond 0.00247 / 0.12 ( 5) SS BOND : angle 0.63585 / 0.37 ( 10) hydrogen bonds : bond 0.03057 / 1.89 ( 74) hydrogen bonds : angle 7.02202 / 4.80 ( 186) link_NAG-ASN : bond 0.00284 / 0.15 ( 1) link_NAG-ASN : angle 1.46037 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8682 (m-30) cc_final: 0.8402 (m-30) REVERT: C 424 LYS cc_start: 0.9080 (tptt) cc_final: 0.8842 (tppp) REVERT: C 444 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8169 (mtmm) REVERT: H 60 ASN cc_start: 0.9020 (t0) cc_final: 0.8807 (t0) REVERT: H 86 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6758 (mtp180) REVERT: H 88 GLU cc_start: 0.9033 (pp20) cc_final: 0.8691 (pp20) REVERT: H 89 ASP cc_start: 0.8157 (m-30) cc_final: 0.7861 (m-30) outliers start: 16 outliers final: 6 residues processed: 76 average time/residue: 0.5413 time to fit residues: 42.0120 Evaluate side-chains 71 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 13 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074013 restraints weight = 5913.851| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.26 r_work: 0.3071 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2556 Z= 0.134 Angle : 0.564 6.877 3482 Z= 0.284 Chirality : 0.043 0.134 370 Planarity : 0.004 0.034 448 Dihedral : 5.065 43.955 352 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.24 % Allowed : 19.85 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.44), residues: 310 helix: -3.31 (1.12), residues: 20 sheet: -0.05 (0.46), residues: 110 loop : -0.70 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 16 TYR 0.009 0.001 TYR H 79 PHE 0.006 0.001 PHE C 347 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 2550) covalent geometry : angle 0.56280 / 0.28 ( 3469) SS BOND : bond 0.00191 / 0.11 ( 5) SS BOND : angle 0.44469 / 0.26 ( 10) hydrogen bonds : bond 0.02667 / 1.65 ( 74) hydrogen bonds : angle 6.74953 / 4.64 ( 186) link_NAG-ASN : bond 0.00264 / 0.14 ( 1) link_NAG-ASN : angle 1.33623 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8632 (m-30) cc_final: 0.8360 (m-30) REVERT: C 424 LYS cc_start: 0.8984 (tptt) cc_final: 0.8707 (tppp) REVERT: C 444 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: H 29 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7388 (t80) REVERT: H 54 ASP cc_start: 0.8934 (t0) cc_final: 0.8723 (p0) REVERT: H 60 ASN cc_start: 0.8982 (t0) cc_final: 0.8775 (t0) REVERT: H 74 SER cc_start: 0.9217 (m) cc_final: 0.8950 (t) REVERT: H 82 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8174 (mtp) REVERT: H 86 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6686 (mtp180) REVERT: H 88 GLU cc_start: 0.9074 (pp20) cc_final: 0.8647 (pp20) REVERT: H 89 ASP cc_start: 0.8130 (m-30) cc_final: 0.7817 (m-30) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 0.3938 time to fit residues: 30.9599 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073747 restraints weight = 5897.850| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.25 r_work: 0.3052 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2556 Z= 0.161 Angle : 0.570 6.189 3482 Z= 0.288 Chirality : 0.043 0.135 370 Planarity : 0.004 0.033 448 Dihedral : 5.043 44.611 352 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 7.12 % Allowed : 20.22 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.44), residues: 310 helix: -3.23 (1.13), residues: 20 sheet: -0.13 (0.49), residues: 98 loop : -0.66 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 16 TYR 0.013 0.001 TYR H 101 PHE 0.007 0.001 PHE C 347 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 2550) covalent geometry : angle 0.56872 / 0.29 ( 3469) SS BOND : bond 0.00226 / 0.12 ( 5) SS BOND : angle 0.41842 / 0.25 ( 10) hydrogen bonds : bond 0.02645 / 1.63 ( 74) hydrogen bonds : angle 6.51485 / 4.51 ( 186) link_NAG-ASN : bond 0.00237 / 0.12 ( 1) link_NAG-ASN : angle 1.42810 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8659 (m-30) cc_final: 0.8370 (m-30) REVERT: C 424 LYS cc_start: 0.9007 (tptt) cc_final: 0.8677 (tppp) REVERT: C 444 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: H 39 GLN cc_start: 0.8076 (pt0) cc_final: 0.7610 (tt0) REVERT: H 60 ASN cc_start: 0.8999 (t0) cc_final: 0.8771 (t0) REVERT: H 74 SER cc_start: 0.9238 (m) cc_final: 0.8964 (t) REVERT: H 82 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: H 86 ARG cc_start: 0.7284 (mtp180) cc_final: 0.6629 (mtp180) REVERT: H 88 GLU cc_start: 0.9053 (pp20) cc_final: 0.8612 (pp20) outliers start: 19 outliers final: 9 residues processed: 81 average time/residue: 0.3791 time to fit residues: 31.4218 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.0050 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.0060 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 474 GLN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074778 restraints weight = 5862.038| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.21 r_work: 0.3082 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2556 Z= 0.121 Angle : 0.593 9.418 3482 Z= 0.289 Chirality : 0.044 0.133 370 Planarity : 0.004 0.035 448 Dihedral : 4.784 40.310 352 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.24 % Allowed : 22.47 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.87 (0.44), residues: 310 helix: -3.32 (1.03), residues: 20 sheet: -0.02 (0.51), residues: 92 loop : -0.51 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 16 TYR 0.008 0.001 TYR C 495 PHE 0.005 0.001 PHE C 347 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 2550) covalent geometry : angle 0.59253 / 0.29 ( 3469) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 0.53509 / 0.28 ( 10) hydrogen bonds : bond 0.02456 / 1.54 ( 74) hydrogen bonds : angle 6.42063 / 4.46 ( 186) link_NAG-ASN : bond 0.00240 / 0.13 ( 1) link_NAG-ASN : angle 1.29748 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8522 (tmm-80) REVERT: C 420 ASP cc_start: 0.8625 (m-30) cc_final: 0.8345 (m-30) REVERT: C 424 LYS cc_start: 0.8959 (tptt) cc_final: 0.8692 (tppp) REVERT: C 444 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: C 516 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6688 (tm-30) REVERT: H 39 GLN cc_start: 0.8058 (pt0) cc_final: 0.7628 (tt0) REVERT: H 50 ASN cc_start: 0.7864 (t0) cc_final: 0.7651 (t0) REVERT: H 60 ASN cc_start: 0.8978 (t0) cc_final: 0.8760 (t0) REVERT: H 74 SER cc_start: 0.9205 (m) cc_final: 0.8936 (t) REVERT: H 82 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: H 86 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6599 (mtp180) REVERT: H 88 GLU cc_start: 0.9105 (pp20) cc_final: 0.8612 (pp20) REVERT: H 89 ASP cc_start: 0.8122 (m-30) cc_final: 0.7846 (m-30) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.4114 time to fit residues: 31.4721 Evaluate side-chains 72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.0010 chunk 1 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 27 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077229 restraints weight = 5836.450| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.25 r_work: 0.3108 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2556 Z= 0.100 Angle : 0.573 8.246 3482 Z= 0.282 Chirality : 0.043 0.133 370 Planarity : 0.004 0.035 448 Dihedral : 4.276 31.538 352 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.24 % Allowed : 23.60 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.78 (0.45), residues: 310 helix: -3.30 (1.00), residues: 20 sheet: 0.20 (0.52), residues: 90 loop : -0.53 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 16 TYR 0.006 0.001 TYR H 79 PHE 0.006 0.001 PHE C 392 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 2550) covalent geometry : angle 0.57192 / 0.28 ( 3469) SS BOND : bond 0.00143 / 0.10 ( 5) SS BOND : angle 0.55375 / 0.30 ( 10) hydrogen bonds : bond 0.02218 / 1.38 ( 74) hydrogen bonds : angle 6.14839 / 4.29 ( 186) link_NAG-ASN : bond 0.00266 / 0.14 ( 1) link_NAG-ASN : angle 1.13072 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: C 403 ARG cc_start: 0.9001 (ttm-80) cc_final: 0.8537 (tmm-80) REVERT: C 408 ARG cc_start: 0.8688 (ptm-80) cc_final: 0.8419 (ptm-80) REVERT: C 420 ASP cc_start: 0.8631 (m-30) cc_final: 0.8388 (m-30) REVERT: C 424 LYS cc_start: 0.8976 (tptt) cc_final: 0.8715 (tppp) REVERT: C 444 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8149 (mtmm) REVERT: C 516 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 517 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7525 (tm) REVERT: H 3 GLN cc_start: 0.8012 (tp40) cc_final: 0.7299 (mp10) REVERT: H 39 GLN cc_start: 0.8065 (pt0) cc_final: 0.7674 (tt0) REVERT: H 60 ASN cc_start: 0.8834 (t0) cc_final: 0.8429 (t0) REVERT: H 74 SER cc_start: 0.9158 (m) cc_final: 0.8913 (t) REVERT: H 82 MET cc_start: 0.8557 (mtm) cc_final: 0.8205 (mtp) REVERT: H 86 ARG cc_start: 0.7290 (mtp180) cc_final: 0.6740 (mtp-110) REVERT: H 88 GLU cc_start: 0.9115 (pp20) cc_final: 0.8592 (pp20) REVERT: H 89 ASP cc_start: 0.7902 (m-30) cc_final: 0.7680 (m-30) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.5722 time to fit residues: 49.5776 Evaluate side-chains 70 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.4957 > 50: distance: 29 - 119: 8.807 distance: 43 - 96: 13.796 distance: 53 - 59: 23.865 distance: 59 - 60: 13.024 distance: 60 - 61: 22.287 distance: 60 - 63: 15.567 distance: 61 - 62: 12.191 distance: 61 - 64: 6.638 distance: 64 - 65: 14.520 distance: 64 - 70: 5.981 distance: 65 - 66: 21.872 distance: 65 - 68: 19.120 distance: 66 - 67: 35.343 distance: 66 - 71: 22.103 distance: 68 - 69: 29.202 distance: 71 - 72: 34.567 distance: 72 - 73: 8.448 distance: 73 - 74: 28.624 distance: 73 - 75: 21.749 distance: 75 - 76: 40.567 distance: 76 - 77: 17.706 distance: 76 - 79: 20.405 distance: 77 - 78: 25.490 distance: 77 - 84: 42.631 distance: 79 - 80: 21.024 distance: 80 - 81: 30.259 distance: 81 - 82: 24.122 distance: 82 - 83: 43.862 distance: 84 - 85: 15.146 distance: 85 - 86: 33.673 distance: 86 - 87: 29.810 distance: 86 - 88: 7.741 distance: 88 - 89: 12.440 distance: 89 - 90: 18.879 distance: 89 - 92: 4.559 distance: 90 - 91: 28.123 distance: 90 - 96: 5.376 distance: 92 - 93: 24.887 distance: 93 - 94: 18.160 distance: 93 - 95: 11.693 distance: 96 - 97: 6.602 distance: 97 - 100: 6.272 distance: 98 - 99: 11.691 distance: 98 - 105: 9.807 distance: 100 - 101: 5.944 distance: 101 - 102: 3.614 distance: 102 - 103: 3.118 distance: 105 - 106: 4.454 distance: 106 - 107: 6.498 distance: 106 - 109: 11.371 distance: 107 - 108: 14.547 distance: 107 - 119: 3.902 distance: 109 - 110: 8.858 distance: 110 - 111: 4.411 distance: 110 - 112: 5.515 distance: 111 - 113: 7.528 distance: 112 - 114: 5.846 distance: 112 - 115: 7.191 distance: 113 - 114: 5.261 distance: 116 - 118: 5.335 distance: 117 - 118: 7.475 distance: 119 - 120: 18.573 distance: 120 - 121: 9.157 distance: 120 - 123: 9.988 distance: 121 - 122: 15.478 distance: 121 - 127: 8.522 distance: 123 - 124: 19.832 distance: 123 - 125: 16.502 distance: 124 - 126: 8.316 distance: 127 - 128: 18.509 distance: 128 - 129: 30.572 distance: 129 - 130: 5.315 distance: 129 - 131: 28.271