Starting phenix.real_space_refine on Tue Feb 3 14:34:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkk_62390/02_2026/9kkk_62390.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkk_62390/02_2026/9kkk_62390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kkk_62390/02_2026/9kkk_62390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkk_62390/02_2026/9kkk_62390.map" model { file = "/net/cci-nas-00/data/ceres_data/9kkk_62390/02_2026/9kkk_62390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkk_62390/02_2026/9kkk_62390.cif" } resolution = 3.85 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2441 2.51 5 N 631 2.21 5 O 659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3761 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3761 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 466} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.04, per 1000 atoms: 0.28 Number of scatterers: 3761 At special positions: 0 Unit cell: (105.375, 63.225, 67.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 659 8.00 N 631 7.00 C 2441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " 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: 0.36 Conformation dependent library (CDL) restraints added in 173.8 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 78.7% alpha, 1.2% 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 2 through 11 Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.895A pdb=" N THR A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.957A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 132 through 160 removed outlier: 3.646A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 180 removed outlier: 3.816A pdb=" N ALA A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 214 Processing helix chain 'A' and resid 219 through 244 removed outlier: 4.312A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 4.234A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.611A pdb=" N HIS A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.545A pdb=" N GLY A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.415A pdb=" N CYS A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 removed outlier: 3.704A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 364' Processing helix chain 'A' and resid 366 through 392 removed outlier: 4.176A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.856A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.939A pdb=" N ARG A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 Proline residue: A 473 - end of helix removed outlier: 3.955A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 499 Proline residue: A 494 - end of helix removed outlier: 4.044A pdb=" N ALA A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.593A pdb=" N SER A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.994A pdb=" N ARG A 80 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 103 " --> pdb=" O ARG A 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 252 hydrogen bonds defined for protein. 738 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: 0.56 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1183 1.34 - 1.46: 583 1.46 - 1.58: 2038 1.58 - 1.70: 0 1.70 - 1.81: 47 Bond restraints: 3851 Sorted by residual: bond pdb=" N ASP A 378 " pdb=" CA ASP A 378 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.19e+00 bond pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 7.01e+00 bond pdb=" N ILE A 226 " pdb=" CA ILE A 226 " ideal model delta sigma weight residual 1.463 1.493 -0.030 1.14e-02 7.69e+03 6.75e+00 bond pdb=" N TYR A 228 " pdb=" CA TYR A 228 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.16e-02 7.43e+03 5.30e+00 bond pdb=" N LEU A 225 " pdb=" CA LEU A 225 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.04e+00 ... (remaining 3846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 5109 1.57 - 3.15: 109 3.15 - 4.72: 21 4.72 - 6.30: 7 6.30 - 7.87: 4 Bond angle restraints: 5250 Sorted by residual: angle pdb=" N ASP A 378 " pdb=" CA ASP A 378 " pdb=" C ASP A 378 " ideal model delta sigma weight residual 111.28 114.93 -3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" CA ILE A 226 " pdb=" C ILE A 226 " pdb=" O ILE A 226 " ideal model delta sigma weight residual 121.41 118.20 3.21 1.04e+00 9.25e-01 9.54e+00 angle pdb=" N THR A 224 " pdb=" CA THR A 224 " pdb=" C THR A 224 " ideal model delta sigma weight residual 111.07 107.78 3.29 1.07e+00 8.73e-01 9.43e+00 angle pdb=" CA GLY A 227 " pdb=" C GLY A 227 " pdb=" O GLY A 227 " ideal model delta sigma weight residual 121.05 118.24 2.81 1.03e+00 9.43e-01 7.45e+00 angle pdb=" CA LEU A 225 " pdb=" C LEU A 225 " pdb=" O LEU A 225 " ideal model delta sigma weight residual 120.90 118.01 2.89 1.07e+00 8.73e-01 7.30e+00 ... (remaining 5245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1928 16.68 - 33.35: 245 33.35 - 50.03: 69 50.03 - 66.70: 18 66.70 - 83.38: 4 Dihedral angle restraints: 2264 sinusoidal: 847 harmonic: 1417 Sorted by residual: dihedral pdb=" CA GLU A 123 " pdb=" CB GLU A 123 " pdb=" CG GLU A 123 " pdb=" CD GLU A 123 " ideal model delta sinusoidal sigma weight residual 60.00 118.56 -58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN A 35 " pdb=" CA ASN A 35 " pdb=" CB ASN A 35 " pdb=" CG ASN A 35 " ideal model delta sinusoidal sigma weight residual -60.00 -118.25 58.25 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LYS A 431 " pdb=" CB LYS A 431 " pdb=" CG LYS A 431 " pdb=" CD LYS A 431 " ideal model delta sinusoidal sigma weight residual -180.00 -122.39 -57.61 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 2261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 434 0.038 - 0.075: 131 0.075 - 0.113: 39 0.113 - 0.151: 6 0.151 - 0.188: 5 Chirality restraints: 615 Sorted by residual: chirality pdb=" CB ILE A 389 " pdb=" CA ILE A 389 " pdb=" CG1 ILE A 389 " pdb=" CG2 ILE A 389 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB ILE A 453 " pdb=" CA ILE A 453 " pdb=" CG1 ILE A 453 " pdb=" CG2 ILE A 453 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA ILE A 226 " pdb=" N ILE A 226 " pdb=" C ILE A 226 " pdb=" CB ILE A 226 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 612 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 67 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.65e+01 pdb=" N PRO A 68 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 50 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 51 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 39 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ASN A 39 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN A 39 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 40 " -0.010 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 28 2.65 - 3.21: 3496 3.21 - 3.77: 5842 3.77 - 4.34: 6982 4.34 - 4.90: 12033 Nonbonded interactions: 28381 Sorted by model distance: nonbonded pdb=" O ARG A 80 " pdb=" OG1 THR A 102 " model vdw 2.087 3.040 nonbonded pdb=" OG SER A 277 " pdb=" OE2 GLU A 316 " model vdw 2.247 3.040 nonbonded pdb=" NE2 HIS A 47 " pdb=" OG SER A 77 " model vdw 2.344 3.120 nonbonded pdb=" N ASP A 418 " pdb=" OD1 ASP A 418 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN A 412 " pdb=" NH1 ARG A 423 " model vdw 2.362 3.120 ... (remaining 28376 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.960 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 0.046 3852 Z= 0.164 Angle : 0.604 7.870 5252 Z= 0.327 Chirality : 0.041 0.188 615 Planarity : 0.006 0.101 660 Dihedral : 16.672 83.376 1349 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 25.13 % Favored : 74.87 % 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: 1.69 (0.41), residues: 485 helix: 1.58 (0.30), residues: 345 sheet: -0.86 (1.62), residues: 10 loop : 0.23 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.016 0.001 TYR A 230 PHE 0.007 0.001 PHE A 3 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3851) covalent geometry : angle 0.60434 ( 5250) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.12652 ( 2) hydrogen bonds : bond 0.11457 ( 252) hydrogen bonds : angle 4.44625 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.143 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0561 time to fit residues: 5.4254 Evaluate side-chains 64 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.163802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139580 restraints weight = 5434.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142411 restraints weight = 3253.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144293 restraints weight = 2278.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145411 restraints weight = 1789.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146248 restraints weight = 1541.499| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3852 Z= 0.118 Angle : 0.531 7.024 5252 Z= 0.263 Chirality : 0.039 0.161 615 Planarity : 0.005 0.069 660 Dihedral : 3.483 13.367 529 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.27 % Allowed : 23.87 % Favored : 72.86 % 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: 1.93 (0.40), residues: 485 helix: 1.83 (0.29), residues: 348 sheet: -1.23 (1.58), residues: 10 loop : 0.07 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.015 0.001 TYR A 264 PHE 0.007 0.001 PHE A 3 TRP 0.005 0.001 TRP A 523 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3851) covalent geometry : angle 0.53128 ( 5250) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.30127 ( 2) hydrogen bonds : bond 0.04392 ( 252) hydrogen bonds : angle 3.80481 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.088 Fit side-chains REVERT: A 131 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7697 (ttm-80) REVERT: A 189 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7140 (t) outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 0.0349 time to fit residues: 3.6094 Evaluate side-chains 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 485 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.156227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131803 restraints weight = 5454.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134361 restraints weight = 3385.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136016 restraints weight = 2458.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136839 restraints weight = 1989.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137695 restraints weight = 1777.123| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3852 Z= 0.145 Angle : 0.555 6.556 5252 Z= 0.277 Chirality : 0.040 0.150 615 Planarity : 0.005 0.055 660 Dihedral : 3.560 13.829 529 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.02 % Allowed : 24.87 % Favored : 71.11 % 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: 1.81 (0.40), residues: 485 helix: 1.75 (0.29), residues: 349 sheet: -1.57 (1.50), residues: 10 loop : 0.01 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.015 0.002 TYR A 264 PHE 0.011 0.001 PHE A 267 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3851) covalent geometry : angle 0.55480 ( 5250) SS BOND : bond 0.00353 ( 1) SS BOND : angle 0.29071 ( 2) hydrogen bonds : bond 0.04977 ( 252) hydrogen bonds : angle 3.90549 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.141 Fit side-chains REVERT: A 31 MET cc_start: 0.8191 (tpt) cc_final: 0.7748 (tpt) REVERT: A 131 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7700 (ttm-80) REVERT: A 169 TYR cc_start: 0.7761 (m-80) cc_final: 0.7528 (m-80) REVERT: A 189 CYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7294 (t) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0627 time to fit residues: 6.1770 Evaluate side-chains 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 61.3034 > 50: distance: 22 - 38: 3.028 distance: 24 - 44: 6.571 distance: 33 - 55: 15.859 distance: 37 - 60: 17.816 distance: 40 - 44: 5.061 distance: 41 - 72: 31.017 distance: 44 - 45: 16.515 distance: 45 - 46: 17.889 distance: 45 - 48: 17.011 distance: 46 - 47: 25.762 distance: 46 - 55: 13.611 distance: 48 - 49: 9.779 distance: 49 - 50: 12.468 distance: 49 - 51: 32.152 distance: 50 - 52: 20.846 distance: 51 - 53: 6.971 distance: 52 - 54: 31.552 distance: 53 - 54: 22.446 distance: 55 - 56: 18.239 distance: 56 - 57: 5.962 distance: 56 - 59: 17.017 distance: 57 - 58: 12.285 distance: 57 - 60: 6.009 distance: 58 - 88: 43.494 distance: 60 - 61: 19.106 distance: 61 - 62: 14.112 distance: 61 - 64: 18.084 distance: 62 - 63: 29.749 distance: 62 - 72: 37.751 distance: 63 - 96: 20.483 distance: 64 - 65: 12.600 distance: 65 - 66: 15.328 distance: 65 - 67: 18.303 distance: 66 - 68: 19.155 distance: 67 - 69: 6.940 distance: 68 - 70: 17.391 distance: 69 - 70: 19.128 distance: 70 - 71: 17.346 distance: 72 - 73: 3.862 distance: 73 - 74: 10.361 distance: 73 - 76: 15.545 distance: 74 - 75: 20.170 distance: 74 - 84: 6.488 distance: 76 - 77: 12.848 distance: 77 - 78: 12.680 distance: 77 - 79: 33.575 distance: 78 - 80: 14.445 distance: 80 - 82: 39.543 distance: 81 - 82: 13.399 distance: 82 - 83: 11.183 distance: 84 - 85: 41.977 distance: 85 - 86: 6.092 distance: 86 - 87: 22.702 distance: 88 - 89: 18.460 distance: 89 - 90: 10.171 distance: 89 - 92: 8.483 distance: 90 - 91: 21.507 distance: 90 - 96: 19.018 distance: 92 - 93: 17.981 distance: 93 - 94: 28.301 distance: 93 - 95: 40.895 distance: 96 - 97: 25.488 distance: 97 - 98: 34.159 distance: 97 - 100: 11.473 distance: 98 - 99: 28.810 distance: 98 - 103: 48.013 distance: 100 - 101: 3.361 distance: 100 - 102: 36.768 distance: 103 - 104: 25.388 distance: 104 - 105: 10.014 distance: 104 - 107: 26.671 distance: 105 - 106: 27.643 distance: 105 - 111: 14.975 distance: 107 - 108: 5.791 distance: 108 - 109: 56.503 distance: 109 - 110: 40.345 distance: 111 - 112: 15.547 distance: 112 - 113: 11.982 distance: 112 - 115: 24.290 distance: 113 - 114: 27.130 distance: 113 - 119: 18.641 distance: 115 - 116: 22.870 distance: 116 - 117: 12.588 distance: 116 - 118: 21.721 distance: 119 - 120: 6.678 distance: 120 - 121: 14.084 distance: 120 - 123: 11.894 distance: 121 - 122: 5.749 distance: 121 - 127: 7.228 distance: 123 - 124: 36.449 distance: 124 - 125: 12.282 distance: 124 - 126: 31.537 distance: 188 - 195: 3.101