Starting phenix.real_space_refine on Tue Feb 3 14:20:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3i_72194/02_2026/9q3i_72194.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3i_72194/02_2026/9q3i_72194.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/9q3i_72194/02_2026/9q3i_72194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3i_72194/02_2026/9q3i_72194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3i_72194/02_2026/9q3i_72194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3i_72194/02_2026/9q3i_72194.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= 0.000 sd= 0.001 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 14 5.16 5 C 2343 2.51 5 N 602 2.21 5 O 676 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: 3635 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3635 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 9 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 21, 'ARG:plan': 7, 'PHE:plan': 4, 'ASP:plan': 11, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 213 Time building chain proxies: 0.98, per 1000 atoms: 0.27 Number of scatterers: 3635 At special positions: 0 Unit cell: (59.92, 60.99, 88.81, 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 14 16.00 O 676 8.00 N 602 7.00 C 2343 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: 0.18 Conformation dependent library (CDL) restraints added in 92.0 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 63.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.760A pdb=" N PHE A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 98 Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.686A pdb=" N ALA A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 259 through 274 Proline residue: A 267 - end of helix removed outlier: 3.746A pdb=" N VAL A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 403 through 424 removed outlier: 3.754A pdb=" N SER A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 453 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.858A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 505 removed outlier: 3.573A pdb=" N PHE A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 542 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 220 hydrogen bonds defined for protein. 645 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: 0.51 Time building geometry restraints manager: 0.25 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: 1146 1.34 - 1.46: 821 1.46 - 1.58: 1720 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3711 Sorted by residual: bond pdb=" N GLU A 519 " pdb=" CA GLU A 519 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.41e-02 5.03e+03 2.92e+00 bond pdb=" CA HIS A 207 " pdb=" C HIS A 207 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.12e-02 7.97e+03 7.88e-01 bond pdb=" N ILE A 154 " pdb=" CA ILE A 154 " ideal model delta sigma weight residual 1.459 1.469 -0.010 1.25e-02 6.40e+03 6.58e-01 bond pdb=" C GLU A 519 " pdb=" O GLU A 519 " ideal model delta sigma weight residual 1.234 1.243 -0.008 1.17e-02 7.31e+03 5.17e-01 bond pdb=" CA GLU A 519 " pdb=" CB GLU A 519 " ideal model delta sigma weight residual 1.532 1.518 0.014 2.01e-02 2.48e+03 5.10e-01 ... (remaining 3706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 4876 1.13 - 2.26: 153 2.26 - 3.39: 21 3.39 - 4.52: 7 4.52 - 5.66: 5 Bond angle restraints: 5062 Sorted by residual: angle pdb=" CA GLU A 519 " pdb=" C GLU A 519 " pdb=" O GLU A 519 " ideal model delta sigma weight residual 121.06 116.31 4.75 1.11e+00 8.12e-01 1.83e+01 angle pdb=" CA GLU A 519 " pdb=" C GLU A 519 " pdb=" N LYS A 520 " ideal model delta sigma weight residual 115.47 119.94 -4.47 1.42e+00 4.96e-01 9.92e+00 angle pdb=" C GLY A 153 " pdb=" N ILE A 154 " pdb=" CA ILE A 154 " ideal model delta sigma weight residual 121.97 127.63 -5.66 1.80e+00 3.09e-01 9.87e+00 angle pdb=" N HIS A 342 " pdb=" CA HIS A 342 " pdb=" CB HIS A 342 " ideal model delta sigma weight residual 113.65 110.62 3.03 1.47e+00 4.63e-01 4.25e+00 angle pdb=" C ASP A 398 " pdb=" N LYS A 399 " pdb=" CA LYS A 399 " ideal model delta sigma weight residual 120.82 123.84 -3.02 1.50e+00 4.44e-01 4.05e+00 ... (remaining 5057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 2030 16.99 - 33.97: 107 33.97 - 50.96: 22 50.96 - 67.94: 5 67.94 - 84.93: 3 Dihedral angle restraints: 2167 sinusoidal: 709 harmonic: 1458 Sorted by residual: dihedral pdb=" CA LYS A 336 " pdb=" C LYS A 336 " pdb=" N GLU A 337 " pdb=" CA GLU A 337 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" N TRP A 266 " pdb=" CA TRP A 266 " pdb=" CB TRP A 266 " pdb=" CG TRP A 266 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 474 " pdb=" CA LEU A 474 " pdb=" CB LEU A 474 " pdb=" CG LEU A 474 " ideal model delta sinusoidal sigma weight residual -180.00 -122.06 -57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 522 0.056 - 0.111: 81 0.111 - 0.167: 1 0.167 - 0.222: 0 0.222 - 0.278: 1 Chirality restraints: 605 Sorted by residual: chirality pdb=" CA GLU A 519 " pdb=" N GLU A 519 " pdb=" C GLU A 519 " pdb=" CB GLU A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA VAL A 521 " pdb=" N VAL A 521 " pdb=" C VAL A 521 " pdb=" CB VAL A 521 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.07e-01 ... (remaining 602 not shown) Planarity restraints: 626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 518 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C VAL A 518 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 518 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 519 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 543 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 544 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 544 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 544 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 216 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 217 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.016 5.00e-02 4.00e+02 ... (remaining 623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 808 2.78 - 3.31: 3785 3.31 - 3.84: 6734 3.84 - 4.37: 7680 4.37 - 4.90: 12926 Nonbonded interactions: 31933 Sorted by model distance: nonbonded pdb=" OD1 ASP A 36 " pdb=" OG SER A 218 " model vdw 2.250 3.040 nonbonded pdb=" N ASP A 202 " pdb=" OD1 ASP A 202 " model vdw 2.305 3.120 nonbonded pdb=" N ASP A 311 " pdb=" OD1 ASP A 311 " model vdw 2.306 3.120 nonbonded pdb=" O SER A 372 " pdb=" OG SER A 375 " model vdw 2.310 3.040 nonbonded pdb=" O TRP A 266 " pdb=" OG1 THR A 270 " model vdw 2.311 3.040 ... (remaining 31928 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.520 Find NCS groups from input model: 0.020 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4074 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 0.024 3711 Z= 0.131 Angle : 0.499 5.656 5062 Z= 0.282 Chirality : 0.038 0.278 605 Planarity : 0.003 0.034 626 Dihedral : 12.075 84.928 1215 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.01 % Favored : 95.36 % Rotamer: Outliers : 4.90 % Allowed : 5.48 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.40), residues: 474 helix: 1.45 (0.31), residues: 295 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 417 TYR 0.011 0.001 TYR A 35 PHE 0.012 0.001 PHE A 480 TRP 0.008 0.001 TRP A 39 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3711) covalent geometry : angle 0.49890 ( 5062) hydrogen bonds : bond 0.14871 ( 220) hydrogen bonds : angle 5.24678 ( 645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 110 average time/residue: 0.4213 time to fit residues: 48.0875 Evaluate side-chains 57 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 347 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.133215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.122141 restraints weight = 7488.669| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.08 r_work: 0.3761 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3711 Z= 0.173 Angle : 0.720 12.193 5062 Z= 0.368 Chirality : 0.043 0.189 605 Planarity : 0.005 0.039 626 Dihedral : 4.331 19.749 522 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.59 % Favored : 95.99 % Rotamer: Outliers : 4.61 % Allowed : 15.85 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.38), residues: 474 helix: 1.24 (0.29), residues: 292 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 383 TYR 0.014 0.002 TYR A 35 PHE 0.013 0.002 PHE A 355 TRP 0.028 0.003 TRP A 460 HIS 0.005 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3711) covalent geometry : angle 0.72015 ( 5062) hydrogen bonds : bond 0.04791 ( 220) hydrogen bonds : angle 4.12071 ( 645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 308 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7386 (t) REVERT: A 311 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8072 (p0) REVERT: A 409 MET cc_start: 0.5087 (ppp) cc_final: 0.4531 (ppp) outliers start: 16 outliers final: 1 residues processed: 67 average time/residue: 0.3957 time to fit residues: 27.7109 Evaluate side-chains 40 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 311 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.132738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.121672 restraints weight = 7586.317| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.05 r_work: 0.3741 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3711 Z= 0.136 Angle : 0.608 7.248 5062 Z= 0.316 Chirality : 0.041 0.179 605 Planarity : 0.004 0.063 626 Dihedral : 4.001 17.663 518 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.16 % Favored : 96.62 % Rotamer: Outliers : 4.03 % Allowed : 19.02 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.38), residues: 474 helix: 1.23 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -1.42 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 383 TYR 0.015 0.002 TYR A 237 PHE 0.014 0.001 PHE A 201 TRP 0.023 0.002 TRP A 230 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3711) covalent geometry : angle 0.60812 ( 5062) hydrogen bonds : bond 0.04117 ( 220) hydrogen bonds : angle 3.93675 ( 645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.184 Fit side-chains REVERT: A 84 ASN cc_start: 0.6505 (m-40) cc_final: 0.6204 (p0) REVERT: A 226 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.7173 (m-70) REVERT: A 409 MET cc_start: 0.6010 (ppp) cc_final: 0.5401 (ppp) outliers start: 14 outliers final: 0 residues processed: 59 average time/residue: 0.3563 time to fit residues: 22.0617 Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.130241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.118688 restraints weight = 7547.736| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.14 r_work: 0.3722 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.9299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3711 Z= 0.159 Angle : 0.673 10.025 5062 Z= 0.348 Chirality : 0.042 0.169 605 Planarity : 0.004 0.049 626 Dihedral : 4.260 18.913 518 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 2.88 % Allowed : 21.90 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.38), residues: 474 helix: 1.26 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -1.19 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 288 TYR 0.023 0.002 TYR A 237 PHE 0.011 0.002 PHE A 55 TRP 0.021 0.003 TRP A 230 HIS 0.004 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3711) covalent geometry : angle 0.67333 ( 5062) hydrogen bonds : bond 0.04321 ( 220) hydrogen bonds : angle 3.88501 ( 645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.138 Fit side-chains REVERT: A 226 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7758 (m90) REVERT: A 284 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7499 (pt) REVERT: A 288 ARG cc_start: 0.5865 (OUTLIER) cc_final: 0.4084 (ppp-140) REVERT: A 409 MET cc_start: 0.6599 (ppp) cc_final: 0.6243 (ppp) REVERT: A 413 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6964 (tt0) outliers start: 10 outliers final: 0 residues processed: 55 average time/residue: 0.3575 time to fit residues: 20.6765 Evaluate side-chains 39 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 413 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 65.083 > 50: distance: 41 - 44: 7.158 distance: 44 - 45: 9.792 distance: 45 - 46: 16.180 distance: 45 - 48: 16.641 distance: 46 - 47: 22.880 distance: 46 - 53: 25.458 distance: 48 - 49: 21.759 distance: 49 - 50: 25.445 distance: 50 - 51: 23.300 distance: 51 - 52: 19.710 distance: 53 - 54: 32.458 distance: 54 - 55: 25.936 distance: 54 - 57: 23.565 distance: 55 - 56: 18.898 distance: 55 - 60: 11.170 distance: 56 - 72: 31.452 distance: 57 - 58: 26.349 distance: 57 - 59: 21.740 distance: 60 - 61: 28.003 distance: 61 - 62: 9.783 distance: 61 - 64: 12.791 distance: 62 - 63: 23.471 distance: 62 - 67: 13.204 distance: 63 - 80: 33.980 distance: 64 - 65: 6.392 distance: 64 - 66: 33.624 distance: 67 - 68: 14.938 distance: 68 - 69: 22.722 distance: 68 - 71: 4.044 distance: 69 - 70: 9.537 distance: 69 - 72: 18.209 distance: 72 - 73: 12.504 distance: 73 - 74: 21.507 distance: 73 - 76: 14.890 distance: 74 - 75: 9.712 distance: 74 - 80: 23.452 distance: 76 - 77: 6.737 distance: 77 - 78: 7.677 distance: 77 - 79: 7.349 distance: 80 - 81: 7.569 distance: 81 - 82: 9.129 distance: 81 - 84: 17.714 distance: 82 - 83: 35.661 distance: 82 - 90: 10.075 distance: 84 - 85: 35.292 distance: 85 - 86: 9.189 distance: 85 - 87: 23.178 distance: 86 - 88: 8.545 distance: 87 - 89: 29.260 distance: 88 - 89: 30.555 distance: 90 - 91: 8.853 distance: 91 - 92: 14.857 distance: 91 - 94: 7.607 distance: 92 - 93: 11.031 distance: 92 - 96: 17.677 distance: 93 - 110: 32.425 distance: 94 - 95: 17.523 distance: 96 - 97: 8.456 distance: 97 - 98: 20.076 distance: 97 - 100: 7.794 distance: 98 - 99: 29.750 distance: 98 - 101: 20.181 distance: 99 - 115: 17.794 distance: 101 - 102: 15.870 distance: 102 - 103: 33.497 distance: 102 - 105: 12.238 distance: 103 - 104: 46.053 distance: 103 - 110: 32.623 distance: 105 - 106: 13.998 distance: 106 - 107: 6.682 distance: 107 - 108: 9.042 distance: 110 - 111: 34.117 distance: 111 - 112: 16.510 distance: 111 - 114: 33.516 distance: 112 - 113: 17.578 distance: 112 - 115: 22.419