Starting phenix.real_space_refine on Wed Jul 1 23:53:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2026/7y7y_33674.cif" } resolution = 2.4 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= 0.109 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2838 2.51 5 N 650 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s 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: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4195 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 108 Unusual residues: {' CL': 1, ' NA': 2, 'ID7': 1, 'NAG': 3} Classifications: {'undetermined': 7, 'water': 54} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.24, per 1000 atoms: 0.29 Number of scatterers: 4303 At special positions: 0 Unit cell: (69.28, 71.445, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 778 8.00 N 650 7.00 C 2838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.05 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 A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 179.0 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.705A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.690A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.985A pdb=" N VAL A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.950A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 4.136A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.619A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.886A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 315 through 350 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.693A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.162A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.937A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.647A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.402A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 571 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 287 hydrogen bonds defined for protein. 840 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: 0.70 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 622 1.31 - 1.44: 1351 1.44 - 1.56: 2354 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4381 Sorted by residual: bond pdb=" C SER A 456 " pdb=" O SER A 456 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" CA SER A 456 " pdb=" CB SER A 456 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.21e+01 bond pdb=" C1 ID7 A 701 " pdb=" O1 ID7 A 701 " ideal model delta sigma weight residual 1.249 1.198 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 ID7 A 701 " pdb=" O2 ID7 A 701 " ideal model delta sigma weight residual 1.248 1.202 0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 ... (remaining 4376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 5856 2.18 - 4.37: 95 4.37 - 6.55: 14 6.55 - 8.73: 2 8.73 - 10.92: 1 Bond angle restraints: 5968 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.22 -10.92 2.00e+00 2.50e-01 2.98e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.74 -8.24 1.70e+00 3.46e-01 2.35e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.56 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CA ASP A 165 " pdb=" CB ASP A 165 " pdb=" CG ASP A 165 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ALA A 455 " pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 116.22 121.73 -5.51 1.44e+00 4.82e-01 1.46e+01 ... (remaining 5963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2089 17.05 - 34.11: 266 34.11 - 51.16: 75 51.16 - 68.22: 19 68.22 - 85.27: 6 Dihedral angle restraints: 2455 sinusoidal: 936 harmonic: 1519 Sorted by residual: dihedral pdb=" CA PHE A 502 " pdb=" C PHE A 502 " pdb=" N PHE A 503 " pdb=" CA PHE A 503 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -54.23 -31.77 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 2452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 662 0.274 - 0.548: 3 0.548 - 0.821: 0 0.821 - 1.095: 0 1.095 - 1.369: 1 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 663 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.008 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" CG ASN A 184 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.191 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.405 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.073 2.00e-02 2.50e+03 7.26e-02 6.60e+01 pdb=" CG ASN A 176 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.116 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.046 2.00e-02 2.50e+03 5.43e-02 3.69e+01 pdb=" CG ASN A 181 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.062 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 31 2.41 - 3.03: 2786 3.03 - 3.66: 6773 3.66 - 4.28: 10892 4.28 - 4.90: 17201 Nonbonded interactions: 37683 Sorted by model distance: nonbonded pdb=" O HOH A 803 " pdb=" O HOH A 822 " model vdw 1.789 3.040 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 805 " model vdw 1.910 3.040 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASP A 287 " pdb=" O HOH A 802 " model vdw 1.987 3.040 nonbonded pdb=" O ALA A 357 " pdb=" O HOH A 803 " model vdw 2.014 3.040 ... (remaining 37678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.640 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: 0.020 Set scattering table: 0.030 Process input model: 6.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.007 0.271 4385 Z= 0.343 Angle : 0.793 18.529 5979 Z= 0.418 Chirality : 0.072 1.369 666 Planarity : 0.005 0.034 722 Dihedral : 17.116 85.271 1488 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 26.56 % Favored : 72.99 % 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: 0.29 (0.36), residues: 525 helix: 0.73 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.11 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 257 TYR 0.027 0.002 TYR A 72 PHE 0.027 0.003 PHE A 398 TRP 0.017 0.002 TRP A 161 HIS 0.005 0.002 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 ( 4381) covalent geometry : angle 0.72532 / 0.40 ( 5968) SS BOND : bond 0.02058 / 1.08 ( 1) SS BOND : angle 6.40781 / 3.57 ( 2) hydrogen bonds : bond 0.13720 / 9.26 ( 287) hydrogen bonds : angle 6.19573 / 4.44 ( 840) link_NAG-ASN : bond 0.16995 / 8.83 ( 3) link_NAG-ASN : angle 7.70618 / 4.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.168 Fit side-chains REVERT: A 572 GLN cc_start: 0.7403 (tp40) cc_final: 0.7069 (tt0) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.6026 time to fit residues: 40.5044 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 487 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS A 483 ASN A 534 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.091543 restraints weight = 4224.343| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.36 r_work: 0.2795 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4385 Z= 0.153 Angle : 0.615 7.847 5979 Z= 0.322 Chirality : 0.044 0.229 666 Planarity : 0.004 0.034 722 Dihedral : 5.278 50.849 587 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 22.77 % Favored : 74.33 % 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: 0.99 (0.37), residues: 525 helix: 1.27 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.023 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4381) covalent geometry : angle 0.60209 / 0.32 ( 5968) SS BOND : bond 0.00289 / 0.15 ( 1) SS BOND : angle 1.56315 / 0.88 ( 2) hydrogen bonds : bond 0.06042 / 4.05 ( 287) hydrogen bonds : angle 4.82342 / 3.50 ( 840) link_NAG-ASN : bond 0.00513 / 0.26 ( 3) link_NAG-ASN : angle 3.21064 / 1.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.163 Fit side-chains REVERT: A 163 GLN cc_start: 0.8590 (mt0) cc_final: 0.8322 (mt0) REVERT: A 485 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: A 559 LEU cc_start: 0.7631 (mt) cc_final: 0.7333 (mt) REVERT: A 572 GLN cc_start: 0.7477 (tp40) cc_final: 0.7030 (tt0) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.5169 time to fit residues: 37.5595 Evaluate side-chains 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090548 restraints weight = 4193.334| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.37 r_work: 0.2776 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4385 Z= 0.169 Angle : 0.629 8.110 5979 Z= 0.329 Chirality : 0.045 0.227 666 Planarity : 0.004 0.036 722 Dihedral : 5.224 52.218 584 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.12 % Allowed : 21.65 % Favored : 75.22 % 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: 1.11 (0.37), residues: 525 helix: 1.39 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.09 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.023 0.002 TYR A 72 PHE 0.030 0.002 PHE A 398 TRP 0.016 0.002 TRP A 116 HIS 0.001 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 4381) covalent geometry : angle 0.61713 / 0.32 ( 5968) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 4.71234 / 2.50 ( 2) hydrogen bonds : bond 0.06287 / 4.21 ( 287) hydrogen bonds : angle 4.81621 / 3.51 ( 840) link_NAG-ASN : bond 0.00415 / 0.20 ( 3) link_NAG-ASN : angle 2.32965 / 1.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.166 Fit side-chains REVERT: A 163 GLN cc_start: 0.8350 (mt0) cc_final: 0.8079 (mt0) REVERT: A 485 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: A 559 LEU cc_start: 0.7727 (mt) cc_final: 0.7499 (mt) REVERT: A 572 GLN cc_start: 0.7479 (tp40) cc_final: 0.7047 (tt0) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.5179 time to fit residues: 38.3180 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.093519 restraints weight = 4177.508| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.34 r_work: 0.2828 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4385 Z= 0.134 Angle : 0.571 8.346 5979 Z= 0.296 Chirality : 0.042 0.197 666 Planarity : 0.004 0.033 722 Dihedral : 5.008 53.009 584 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 22.10 % Favored : 75.00 % 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: 1.33 (0.37), residues: 525 helix: 1.55 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.10 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.021 0.001 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.013 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4381) covalent geometry : angle 0.56199 / 0.29 ( 5968) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 3.67765 / 1.94 ( 2) hydrogen bonds : bond 0.05377 / 3.60 ( 287) hydrogen bonds : angle 4.60533 / 3.35 ( 840) link_NAG-ASN : bond 0.00371 / 0.18 ( 3) link_NAG-ASN : angle 2.09857 / 1.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.166 Fit side-chains REVERT: A 163 GLN cc_start: 0.8283 (mt0) cc_final: 0.8041 (mt0) REVERT: A 348 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 559 LEU cc_start: 0.7866 (mt) cc_final: 0.7493 (mt) REVERT: A 572 GLN cc_start: 0.7470 (tp40) cc_final: 0.7018 (tt0) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.4691 time to fit residues: 35.1705 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.092879 restraints weight = 4220.577| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.35 r_work: 0.2820 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4385 Z= 0.139 Angle : 0.572 9.162 5979 Z= 0.296 Chirality : 0.043 0.182 666 Planarity : 0.004 0.032 722 Dihedral : 4.999 53.496 584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.68 % Allowed : 21.43 % Favored : 75.89 % 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: 1.36 (0.37), residues: 525 helix: 1.58 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.09 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.022 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.013 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4381) covalent geometry : angle 0.56631 / 0.29 ( 5968) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 3.13462 / 1.66 ( 2) hydrogen bonds : bond 0.05505 / 3.69 ( 287) hydrogen bonds : angle 4.59396 / 3.34 ( 840) link_NAG-ASN : bond 0.00346 / 0.17 ( 3) link_NAG-ASN : angle 1.65754 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.172 Fit side-chains REVERT: A 163 GLN cc_start: 0.8285 (mt0) cc_final: 0.8082 (mt0) REVERT: A 172 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7340 (mtp-110) REVERT: A 348 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8297 (t) REVERT: A 485 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: A 559 LEU cc_start: 0.7948 (mt) cc_final: 0.7568 (mt) REVERT: A 572 GLN cc_start: 0.7499 (tp40) cc_final: 0.7045 (tt0) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.5135 time to fit residues: 39.5282 Evaluate side-chains 72 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093032 restraints weight = 4312.963| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.35 r_work: 0.2823 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4385 Z= 0.140 Angle : 0.577 9.678 5979 Z= 0.297 Chirality : 0.043 0.179 666 Planarity : 0.004 0.033 722 Dihedral : 4.982 53.666 584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.12 % Allowed : 20.76 % Favored : 76.12 % 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: 1.40 (0.37), residues: 525 helix: 1.58 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -1.03 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.022 0.002 TYR A 72 PHE 0.029 0.002 PHE A 398 TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4381) covalent geometry : angle 0.57195 / 0.30 ( 5968) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 2.99450 / 1.58 ( 2) hydrogen bonds : bond 0.05491 / 3.68 ( 287) hydrogen bonds : angle 4.58066 / 3.33 ( 840) link_NAG-ASN : bond 0.00336 / 0.16 ( 3) link_NAG-ASN : angle 1.58394 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.163 Fit side-chains REVERT: A 163 GLN cc_start: 0.8328 (mt0) cc_final: 0.8119 (mt0) REVERT: A 172 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7224 (mtp-110) REVERT: A 348 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8216 (t) REVERT: A 485 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: A 559 LEU cc_start: 0.7885 (mt) cc_final: 0.7499 (mt) REVERT: A 572 GLN cc_start: 0.7475 (tp40) cc_final: 0.7012 (tt0) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.5165 time to fit residues: 39.2775 Evaluate side-chains 82 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 67.7344 > 50: distance: 0 - 10: 3.004 distance: 18 - 24: 26.142 distance: 24 - 25: 9.195 distance: 24 - 30: 13.453 distance: 25 - 26: 18.105 distance: 25 - 28: 14.752 distance: 26 - 27: 42.378 distance: 28 - 29: 12.151 distance: 29 - 30: 5.731 distance: 31 - 32: 24.164 distance: 32 - 33: 47.564 distance: 32 - 35: 11.907 distance: 33 - 34: 27.310 distance: 33 - 45: 45.214 distance: 35 - 36: 3.054 distance: 36 - 37: 9.364 distance: 36 - 38: 18.556 distance: 37 - 39: 19.365 distance: 38 - 40: 35.760 distance: 38 - 41: 27.378 distance: 39 - 40: 30.980 distance: 40 - 42: 40.531 distance: 41 - 43: 30.316 distance: 42 - 44: 26.205 distance: 43 - 44: 8.790 distance: 45 - 46: 20.096 distance: 46 - 47: 18.688 distance: 46 - 49: 29.186 distance: 47 - 48: 17.833 distance: 47 - 54: 15.334 distance: 49 - 50: 51.392 distance: 50 - 51: 30.881 distance: 51 - 52: 28.829 distance: 52 - 53: 44.059 distance: 54 - 55: 25.903 distance: 55 - 56: 29.419 distance: 55 - 58: 22.775 distance: 56 - 57: 41.863 distance: 56 - 63: 12.442 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