Starting phenix.real_space_refine on Tue Feb 3 15:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9km3_62421/02_2026/9km3_62421.cif Found real_map, /net/cci-nas-00/data/ceres_data/9km3_62421/02_2026/9km3_62421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9km3_62421/02_2026/9km3_62421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9km3_62421/02_2026/9km3_62421.map" model { file = "/net/cci-nas-00/data/ceres_data/9km3_62421/02_2026/9km3_62421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9km3_62421/02_2026/9km3_62421.cif" } resolution = 2.9 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= 0.041 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 36 5.16 5 Cl 1 4.86 5 Na 3 4.78 5 C 2833 2.51 5 N 617 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4185 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4146 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 39 Unusual residues: {' CL': 1, ' NA': 3, 'CLR': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 805 "'] Classifications: {'peptide': 1, 'undetermined': 5, 'water': 2} Modifications used: {'COO': 1} Link IDs: {None: 7} Time building chain proxies: 0.92, per 1000 atoms: 0.22 Number of scatterers: 4185 At special positions: 0 Unit cell: (83.3, 65.45, 85.85, 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 36 16.00 Na 3 11.00 O 695 8.00 N 617 7.00 C 2833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 312 " 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 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 151.9 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 76.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 202 through 207 removed outlier: 4.036A pdb=" N VAL A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.802A pdb=" N TYR A 211 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.997A pdb=" N ALA A 257 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 293 removed outlier: 3.892A pdb=" N GLY A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 385 through 406 Processing helix chain 'A' and resid 413 through 434 removed outlier: 3.695A pdb=" N THR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Proline residue: A 421 - end of helix removed outlier: 4.003A pdb=" N THR A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.760A pdb=" N GLY A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 489 through 524 Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.582A pdb=" N VAL A 530 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 547 Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 551 through 586 removed outlier: 3.521A pdb=" N TRP A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.603A pdb=" N HIS A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 594' Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.020A pdb=" N LEU A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 616 through 628 removed outlier: 4.066A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 647 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.663A pdb=" N MET A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.585A pdb=" N LYS A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.780A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 719 removed outlier: 3.610A pdb=" N MET A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.775A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 696 through 697 262 hydrogen bonds defined for protein. 771 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: 0.47 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1179 1.34 - 1.46: 1125 1.46 - 1.58: 1957 1.58 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 4320 Sorted by residual: bond pdb=" C8 CLR A 804 " pdb=" C9 CLR A 804 " ideal model delta sigma weight residual 1.535 1.490 0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C14 CLR A 804 " pdb=" C15 CLR A 804 " ideal model delta sigma weight residual 1.523 1.478 0.045 2.00e-02 2.50e+03 4.99e+00 bond pdb=" C20 CLR A 804 " pdb=" C22 CLR A 804 " ideal model delta sigma weight residual 1.535 1.495 0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C GLU A 365 " pdb=" N TYR A 366 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.40e-02 5.10e+03 3.57e+00 bond pdb=" C3 CLR A 804 " pdb=" C4 CLR A 804 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 4315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 5854 3.13 - 6.26: 34 6.26 - 9.40: 6 9.40 - 12.53: 7 12.53 - 15.66: 3 Bond angle restraints: 5904 Sorted by residual: angle pdb=" C12 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C17 CLR A 804 " ideal model delta sigma weight residual 116.52 100.86 15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C14 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C18 CLR A 804 " ideal model delta sigma weight residual 112.24 127.55 -15.31 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C4 CLR A 804 " pdb=" C5 CLR A 804 " pdb=" C6 CLR A 804 " ideal model delta sigma weight residual 120.33 133.03 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C16 CLR A 804 " pdb=" C17 CLR A 804 " pdb=" C20 CLR A 804 " ideal model delta sigma weight residual 112.02 124.33 -12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C1 CLR A 804 " pdb=" C10 CLR A 804 " pdb=" C9 CLR A 804 " ideal model delta sigma weight residual 108.36 96.50 11.86 3.00e+00 1.11e-01 1.56e+01 ... (remaining 5899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 2226 21.64 - 43.28: 216 43.28 - 64.91: 56 64.91 - 86.55: 3 86.55 - 108.19: 4 Dihedral angle restraints: 2505 sinusoidal: 985 harmonic: 1520 Sorted by residual: dihedral pdb=" CA GLU A 365 " pdb=" C GLU A 365 " pdb=" N TYR A 366 " pdb=" CA TYR A 366 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C10 CLR A 804 " pdb=" C1 CLR A 804 " pdb=" C2 CLR A 804 " pdb=" C3 CLR A 804 " ideal model delta sinusoidal sigma weight residual -56.83 51.36 -108.19 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C1 CLR A 804 " pdb=" C2 CLR A 804 " pdb=" C3 CLR A 804 " pdb=" O1 CLR A 804 " ideal model delta sinusoidal sigma weight residual 180.04 72.52 107.52 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 2502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 660 0.112 - 0.223: 6 0.223 - 0.335: 1 0.335 - 0.447: 1 0.447 - 0.559: 1 Chirality restraints: 669 Sorted by residual: chirality pdb=" C20 CLR A 804 " pdb=" C17 CLR A 804 " pdb=" C21 CLR A 804 " pdb=" C22 CLR A 804 " both_signs ideal model delta sigma weight residual False 2.59 2.03 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C9 CLR A 804 " pdb=" C10 CLR A 804 " pdb=" C11 CLR A 804 " pdb=" C8 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.45 -2.80 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C13 CLR A 804 " pdb=" C12 CLR A 804 " pdb=" C14 CLR A 804 " pdb=" C17 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.93 -3.18 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 666 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 258 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 259 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 366 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C TYR A 366 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR A 366 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 367 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 610 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 611 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.018 5.00e-02 4.00e+02 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 723 2.76 - 3.29: 3890 3.29 - 3.83: 6900 3.83 - 4.36: 7640 4.36 - 4.90: 14053 Nonbonded interactions: 33206 Sorted by model distance: nonbonded pdb=" OE1 GLU A 640 " pdb="NA NA A 808 " model vdw 2.225 2.470 nonbonded pdb=" OD1 ASN A 205 " pdb="NA NA A 806 " model vdw 2.320 2.470 nonbonded pdb=" O VAL A 201 " pdb="NA NA A 807 " model vdw 2.326 2.470 nonbonded pdb=" OG1 THR A 570 " pdb="NA NA A 807 " model vdw 2.334 2.470 nonbonded pdb=" OE2 GLU A 240 " pdb="NA NA A 808 " model vdw 2.337 2.470 ... (remaining 33201 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: 1.080 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.550 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.003 0.045 4321 Z= 0.162 Angle : 0.796 15.659 5906 Z= 0.350 Chirality : 0.050 0.559 669 Planarity : 0.005 0.067 703 Dihedral : 17.891 108.188 1530 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.68 % Allowed : 27.03 % Favored : 72.30 % 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: 1.16 (0.38), residues: 519 helix: 1.81 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 652 TYR 0.020 0.001 TYR A 278 PHE 0.021 0.001 PHE A 572 TRP 0.009 0.001 TRP A 705 HIS 0.000 0.000 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4320) covalent geometry : angle 0.79654 ( 5904) SS BOND : bond 0.00102 ( 1) SS BOND : angle 0.49430 ( 2) hydrogen bonds : bond 0.14578 ( 262) hydrogen bonds : angle 5.26833 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.148 Fit side-chains REVERT: A 249 GLN cc_start: 0.7550 (mt0) cc_final: 0.7130 (mt0) REVERT: A 544 GLU cc_start: 0.7345 (tp30) cc_final: 0.7133 (tp30) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.3323 time to fit residues: 27.6791 Evaluate side-chains 66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 632 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125142 restraints weight = 5170.702| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.16 r_work: 0.3333 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4321 Z= 0.138 Angle : 0.558 6.045 5906 Z= 0.284 Chirality : 0.042 0.132 669 Planarity : 0.004 0.046 703 Dihedral : 10.639 100.454 624 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 24.32 % Favored : 72.52 % 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: 1.31 (0.38), residues: 519 helix: 1.89 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -1.81 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.020 0.001 TYR A 278 PHE 0.015 0.001 PHE A 687 TRP 0.010 0.001 TRP A 474 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4320) covalent geometry : angle 0.55783 ( 5904) SS BOND : bond 0.00359 ( 1) SS BOND : angle 1.13585 ( 2) hydrogen bonds : bond 0.05952 ( 262) hydrogen bonds : angle 4.04654 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.107 Fit side-chains REVERT: A 249 GLN cc_start: 0.7503 (mt0) cc_final: 0.7147 (mt0) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 0.3581 time to fit residues: 29.0118 Evaluate side-chains 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122704 restraints weight = 5139.407| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.21 r_work: 0.3333 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4321 Z= 0.123 Angle : 0.551 7.307 5906 Z= 0.276 Chirality : 0.042 0.125 669 Planarity : 0.004 0.039 703 Dihedral : 8.731 82.281 623 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.93 % Allowed : 23.65 % Favored : 73.42 % 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: 1.45 (0.38), residues: 519 helix: 1.98 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.77 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 208 TYR 0.019 0.001 TYR A 278 PHE 0.023 0.001 PHE A 572 TRP 0.008 0.001 TRP A 705 HIS 0.001 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4320) covalent geometry : angle 0.55050 ( 5904) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.90071 ( 2) hydrogen bonds : bond 0.05475 ( 262) hydrogen bonds : angle 3.90609 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.165 Fit side-chains REVERT: A 249 GLN cc_start: 0.7019 (mt0) cc_final: 0.6710 (mt0) REVERT: A 383 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6847 (mt-10) outliers start: 13 outliers final: 4 residues processed: 70 average time/residue: 0.3578 time to fit residues: 26.4373 Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 623 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120198 restraints weight = 5189.974| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.32 r_work: 0.3297 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4321 Z= 0.136 Angle : 0.571 8.034 5906 Z= 0.286 Chirality : 0.043 0.134 669 Planarity : 0.004 0.034 703 Dihedral : 7.761 73.122 623 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.60 % Allowed : 22.97 % Favored : 73.42 % 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: 1.35 (0.38), residues: 519 helix: 1.98 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.87 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.021 0.001 TYR A 278 PHE 0.020 0.001 PHE A 586 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4320) covalent geometry : angle 0.57045 ( 5904) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.07693 ( 2) hydrogen bonds : bond 0.05971 ( 262) hydrogen bonds : angle 3.92283 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.162 Fit side-chains REVERT: A 729 MET cc_start: 0.7261 (tpp) cc_final: 0.7058 (mmp) REVERT: A 753 PHE cc_start: 0.7150 (t80) cc_final: 0.6935 (t80) outliers start: 16 outliers final: 7 residues processed: 71 average time/residue: 0.2875 time to fit residues: 21.7258 Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 704 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119761 restraints weight = 5155.247| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.31 r_work: 0.3244 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4321 Z= 0.135 Angle : 0.553 5.964 5906 Z= 0.283 Chirality : 0.043 0.175 669 Planarity : 0.004 0.033 703 Dihedral : 5.408 55.617 623 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.38 % Allowed : 23.42 % Favored : 73.20 % 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: 1.26 (0.38), residues: 519 helix: 1.88 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.94 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.020 0.001 TYR A 278 PHE 0.015 0.001 PHE A 687 TRP 0.009 0.001 TRP A 255 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4320) covalent geometry : angle 0.55300 ( 5904) SS BOND : bond 0.00232 ( 1) SS BOND : angle 1.06894 ( 2) hydrogen bonds : bond 0.05966 ( 262) hydrogen bonds : angle 3.90923 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.161 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 76 average time/residue: 0.2714 time to fit residues: 21.8062 Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126658 restraints weight = 5338.160| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.11 r_work: 0.3347 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4321 Z= 0.130 Angle : 0.550 8.972 5906 Z= 0.283 Chirality : 0.042 0.185 669 Planarity : 0.004 0.030 703 Dihedral : 5.091 54.944 623 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.15 % Allowed : 24.77 % Favored : 72.07 % 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: 1.31 (0.38), residues: 519 helix: 1.90 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.90 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 548 TYR 0.020 0.001 TYR A 278 PHE 0.017 0.001 PHE A 687 TRP 0.009 0.001 TRP A 255 HIS 0.002 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4320) covalent geometry : angle 0.54966 ( 5904) SS BOND : bond 0.00211 ( 1) SS BOND : angle 1.11427 ( 2) hydrogen bonds : bond 0.05766 ( 262) hydrogen bonds : angle 3.88556 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.094 Fit side-chains REVERT: A 729 MET cc_start: 0.7460 (tpp) cc_final: 0.7214 (mmp) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.2345 time to fit residues: 18.5984 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6684 > 50: distance: 58 - 74: 27.648 distance: 69 - 74: 27.719 distance: 74 - 75: 44.163 distance: 75 - 76: 43.839 distance: 75 - 78: 41.919 distance: 76 - 77: 46.901 distance: 76 - 86: 25.363 distance: 77 - 107: 3.400 distance: 78 - 79: 43.679 distance: 79 - 80: 40.970 distance: 79 - 81: 57.225 distance: 80 - 82: 41.917 distance: 81 - 83: 37.895 distance: 82 - 84: 27.572 distance: 83 - 84: 12.840 distance: 84 - 85: 49.705 distance: 86 - 87: 13.541 distance: 86 - 92: 43.190 distance: 87 - 90: 39.475 distance: 88 - 89: 37.987 distance: 88 - 93: 17.478 distance: 89 - 115: 39.321 distance: 90 - 91: 41.367 distance: 91 - 92: 27.050 distance: 93 - 94: 41.080 distance: 94 - 95: 10.017 distance: 94 - 97: 55.673 distance: 95 - 96: 17.160 distance: 95 - 102: 40.059 distance: 97 - 98: 41.121 distance: 98 - 99: 34.449 distance: 99 - 101: 56.236 distance: 102 - 103: 26.261 distance: 103 - 106: 26.773 distance: 104 - 107: 56.193 distance: 107 - 108: 39.022 distance: 108 - 109: 57.880 distance: 108 - 111: 5.169 distance: 109 - 110: 39.374 distance: 109 - 115: 56.004 distance: 111 - 112: 51.847 distance: 112 - 113: 39.335 distance: 115 - 116: 39.330 distance: 116 - 117: 70.694 distance: 117 - 118: 68.385 distance: 117 - 122: 55.205 distance: 119 - 120: 40.909 distance: 119 - 121: 38.958 distance: 122 - 123: 11.941 distance: 123 - 124: 37.750 distance: 123 - 126: 42.068 distance: 124 - 125: 10.964 distance: 124 - 133: 46.738 distance: 126 - 127: 58.046 distance: 127 - 128: 40.961 distance: 128 - 129: 40.353 distance: 129 - 130: 33.161 distance: 130 - 131: 21.777 distance: 130 - 132: 46.343 distance: 134 - 135: 58.887 distance: 134 - 137: 40.816 distance: 135 - 136: 15.381 distance: 135 - 141: 14.001 distance: 137 - 138: 39.154 distance: 138 - 140: 57.714 distance: 141 - 147: 57.460 distance: 142 - 143: 14.845 distance: 142 - 145: 40.938 distance: 143 - 144: 59.951 distance: 143 - 148: 57.985 distance: 146 - 147: 38.648 distance: 148 - 149: 33.398 distance: 149 - 150: 24.825 distance: 149 - 152: 50.833 distance: 150 - 151: 35.800 distance: 150 - 156: 24.083 distance: 152 - 153: 65.582 distance: 153 - 154: 40.917 distance: 153 - 155: 67.426