Starting phenix.real_space_refine on Fri Aug 22 13:17:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcs_18334/08_2025/8qcs_18334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcs_18334/08_2025/8qcs_18334.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 { model { file = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2025/8qcs_18334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2025/8qcs_18334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2025/8qcs_18334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2025/8qcs_18334.map" } 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= 0.003 sd= 0.097 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 18 5.16 5 C 2156 2.51 5 N 500 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3241 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 17, 'TRANS': 399} Time building chain proxies: 1.01, per 1000 atoms: 0.31 Number of scatterers: 3241 At special positions: 0 Unit cell: (80.22, 55.008, 65.322, 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 18 16.00 O 567 8.00 N 500 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.29 Conformation dependent library (CDL) restraints added in 97.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.213A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.068A pdb=" N GLY A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.719A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.722A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.712A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.555A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.349A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.502A pdb=" N THR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.777A pdb=" N ASP A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 6.226A pdb=" N GLU A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU A 318 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.542A pdb=" N PHE A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 3.709A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.112A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.518A pdb=" N MET A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.721A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.768A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.556A pdb=" N LEU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 756 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: 0.37 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: 961 1.34 - 1.46: 641 1.46 - 1.57: 1693 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3323 Sorted by residual: bond pdb=" N ILE A 427 " pdb=" CA ILE A 427 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.52e+00 bond pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.28e+00 bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.33e-02 5.65e+03 4.95e+00 bond pdb=" CB GLN A 306 " pdb=" CG GLN A 306 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C ILE A 427 " pdb=" N VAL A 428 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.20e-02 6.94e+03 8.92e-01 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4444 1.69 - 3.39: 66 3.39 - 5.08: 16 5.08 - 6.77: 7 6.77 - 8.47: 1 Bond angle restraints: 4534 Sorted by residual: angle pdb=" C ALA A 307 " pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.23e+00 angle pdb=" N GLN A 308 " pdb=" CA GLN A 308 " pdb=" C GLN A 308 " ideal model delta sigma weight residual 112.23 108.88 3.35 1.26e+00 6.30e-01 7.09e+00 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 115.56 -5.75 2.21e+00 2.05e-01 6.76e+00 angle pdb=" N LYS A 396 " pdb=" CA LYS A 396 " pdb=" C LYS A 396 " ideal model delta sigma weight residual 108.34 111.55 -3.21 1.31e+00 5.83e-01 6.02e+00 angle pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " pdb=" CG LEU A 269 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.85e+00 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 1697 17.51 - 35.02: 168 35.02 - 52.53: 34 52.53 - 70.05: 13 70.05 - 87.56: 2 Dihedral angle restraints: 1914 sinusoidal: 714 harmonic: 1200 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -86.73 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR A 440 " pdb=" C THR A 440 " pdb=" N GLY A 441 " pdb=" CA GLY A 441 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 316 0.026 - 0.051: 130 0.051 - 0.077: 66 0.077 - 0.102: 23 0.102 - 0.128: 8 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA TYR A 117 " pdb=" N TYR A 117 " pdb=" C TYR A 117 " pdb=" CB TYR A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 540 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 444 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 255 " -0.020 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 256 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 256 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 257 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " 0.015 5.00e-02 4.00e+02 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1003 2.82 - 3.34: 3277 3.34 - 3.86: 5409 3.86 - 4.38: 6478 4.38 - 4.90: 10937 Nonbonded interactions: 27104 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLU A 367 " model vdw 2.301 3.120 nonbonded pdb=" O ILE A 415 " pdb=" OG1 THR A 419 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OG SER A 458 " model vdw 2.383 3.040 nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 508 " model vdw 2.419 3.040 nonbonded pdb=" NE1 TRP A 189 " pdb=" OG1 THR A 286 " model vdw 2.424 3.120 ... (remaining 27099 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.270 Find NCS groups from input model: 0.010 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 0.036 3323 Z= 0.136 Angle : 0.571 8.467 4534 Z= 0.294 Chirality : 0.038 0.128 543 Planarity : 0.003 0.034 550 Dihedral : 15.225 87.558 1150 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 20.11 % Favored : 79.89 % 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 aren not related in a simple way. whole: 0.62 (0.39), residues: 415 helix: 0.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.18 (0.58), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.016 0.001 TYR A 117 PHE 0.008 0.001 PHE A 162 TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3323) covalent geometry : angle 0.57116 ( 4534) hydrogen bonds : bond 0.24584 ( 255) hydrogen bonds : angle 7.70171 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.6068 time to fit residues: 24.8969 Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105514 restraints weight = 4136.655| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.21 r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.146 Angle : 0.617 8.103 4534 Z= 0.315 Chirality : 0.040 0.153 543 Planarity : 0.004 0.030 550 Dihedral : 4.142 15.287 446 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 18.70 % Favored : 79.60 % 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 aren not related in a simple way. whole: 1.55 (0.41), residues: 415 helix: 1.67 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.69 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.010 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3323) covalent geometry : angle 0.61706 ( 4534) hydrogen bonds : bond 0.05183 ( 255) hydrogen bonds : angle 4.85555 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.136 Fit side-chains REVERT: A 136 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6508 (mt-10) REVERT: A 169 ASP cc_start: 0.7603 (m-30) cc_final: 0.7225 (m-30) REVERT: A 277 MET cc_start: 0.7864 (ttp) cc_final: 0.7660 (ttm) REVERT: A 390 LEU cc_start: 0.7484 (mt) cc_final: 0.6722 (tt) REVERT: A 409 SER cc_start: 0.9063 (t) cc_final: 0.8810 (m) outliers start: 6 outliers final: 0 residues processed: 53 average time/residue: 0.5442 time to fit residues: 29.7188 Evaluate side-chains 42 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104758 restraints weight = 4084.355| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.18 r_work: 0.3053 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3323 Z= 0.145 Angle : 0.588 7.278 4534 Z= 0.299 Chirality : 0.040 0.149 543 Planarity : 0.004 0.030 550 Dihedral : 4.065 15.223 446 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.55 % Allowed : 19.26 % Favored : 78.19 % 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 aren not related in a simple way. whole: 1.80 (0.41), residues: 415 helix: 1.90 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.79 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.009 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3323) covalent geometry : angle 0.58774 ( 4534) hydrogen bonds : bond 0.04717 ( 255) hydrogen bonds : angle 4.58044 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.123 Fit side-chains REVERT: A 136 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: A 277 MET cc_start: 0.7835 (ttp) cc_final: 0.7616 (ttm) REVERT: A 390 LEU cc_start: 0.7580 (mt) cc_final: 0.6799 (tt) REVERT: A 409 SER cc_start: 0.9044 (t) cc_final: 0.8811 (m) outliers start: 9 outliers final: 1 residues processed: 48 average time/residue: 0.5460 time to fit residues: 27.0710 Evaluate side-chains 43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 413 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8162 > 50: distance: 37 - 50: 3.022 distance: 39 - 56: 5.455 distance: 43 - 61: 27.946 distance: 49 - 68: 30.307 distance: 52 - 56: 3.685 distance: 53 - 73: 15.773 distance: 56 - 57: 6.551 distance: 57 - 58: 13.884 distance: 57 - 60: 11.425 distance: 58 - 59: 10.214 distance: 58 - 61: 14.883 distance: 59 - 80: 15.786 distance: 61 - 62: 5.335 distance: 62 - 63: 17.648 distance: 62 - 65: 5.801 distance: 63 - 64: 23.130 distance: 63 - 68: 17.657 distance: 64 - 88: 12.396 distance: 65 - 66: 11.981 distance: 65 - 67: 21.893 distance: 68 - 69: 49.754 distance: 69 - 70: 18.395 distance: 69 - 72: 14.185 distance: 70 - 71: 14.145 distance: 70 - 73: 14.839 distance: 71 - 92: 22.226 distance: 73 - 74: 7.488 distance: 74 - 75: 9.376 distance: 74 - 77: 9.352 distance: 75 - 76: 7.169 distance: 75 - 80: 6.359 distance: 76 - 100: 4.408 distance: 77 - 78: 6.970 distance: 77 - 79: 24.904 distance: 80 - 81: 9.443 distance: 81 - 82: 4.161 distance: 81 - 84: 14.809 distance: 82 - 83: 3.584 distance: 82 - 88: 5.348 distance: 83 - 109: 4.610 distance: 84 - 85: 5.275 distance: 85 - 86: 7.956 distance: 85 - 87: 6.800 distance: 90 - 91: 8.195 distance: 90 - 92: 5.964 distance: 91 - 117: 15.340 distance: 92 - 93: 4.889 distance: 93 - 94: 5.371 distance: 94 - 95: 6.298 distance: 94 - 100: 4.331 distance: 96 - 97: 7.888 distance: 97 - 98: 3.529 distance: 97 - 99: 4.758 distance: 101 - 102: 3.931 distance: 101 - 104: 7.205 distance: 102 - 103: 8.648 distance: 103 - 128: 9.707 distance: 104 - 105: 3.127 distance: 105 - 106: 4.470 distance: 106 - 107: 3.376 distance: 106 - 108: 6.240 distance: 109 - 110: 5.397 distance: 110 - 113: 6.896 distance: 111 - 112: 3.303 distance: 112 - 133: 8.174 distance: 113 - 114: 3.743 distance: 114 - 115: 22.647 distance: 114 - 116: 16.730 distance: 117 - 118: 4.443 distance: 118 - 119: 6.455 distance: 119 - 121: 7.869 distance: 120 - 140: 6.565