Starting phenix.real_space_refine on Fri Aug 22 15:22:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1d_36792/08_2025/8k1d_36792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1d_36792/08_2025/8k1d_36792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1d_36792/08_2025/8k1d_36792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1d_36792/08_2025/8k1d_36792.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1d_36792/08_2025/8k1d_36792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1d_36792/08_2025/8k1d_36792.cif" } resolution = 3.53 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= 0.006 sd= 0.102 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 38 5.16 5 C 3310 2.51 5 N 758 2.21 5 O 796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s 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: 4902 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2451 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2451 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 1.55, per 1000 atoms: 0.32 Number of scatterers: 4902 At special positions: 0 Unit cell: (93.15, 71.55, 74.25, 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 38 16.00 O 796 8.00 N 758 7.00 C 3310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " 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: 0.41 Conformation dependent library (CDL) restraints added in 186.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 302 through 333 removed outlier: 3.895A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 524 removed outlier: 3.663A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 4.170A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 586 removed outlier: 3.854A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 644 removed outlier: 3.615A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 Processing helix chain 'A' and resid 708 through 735 Processing helix chain 'A' and resid 744 through 762 removed outlier: 3.893A pdb=" N ALA A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.862A pdb=" N LYS A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 809 Processing helix chain 'B' and resid 302 through 333 removed outlier: 3.804A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 474 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.713A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 4.145A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 586 removed outlier: 3.901A pdb=" N GLN B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 644 removed outlier: 3.673A pdb=" N SER B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 705 Processing helix chain 'B' and resid 708 through 735 removed outlier: 3.920A pdb=" N TYR B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 762 removed outlier: 3.755A pdb=" N ALA B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 789 through 809 381 hydrogen bonds defined for protein. 1143 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: 0.77 Time building geometry restraints manager: 0.58 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: 1396 1.34 - 1.46: 1174 1.46 - 1.58: 2414 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 5042 Sorted by residual: bond pdb=" C CYS B 565 " pdb=" N PRO B 566 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 7.99e+00 bond pdb=" C CYS A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.11e-02 8.12e+03 5.39e+00 bond pdb=" N LEU B 512 " pdb=" CA LEU B 512 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.32e+00 bond pdb=" C PRO B 566 " pdb=" O PRO B 566 " ideal model delta sigma weight residual 1.233 1.217 0.016 9.60e-03 1.09e+04 2.76e+00 bond pdb=" C PRO A 566 " pdb=" O PRO A 566 " ideal model delta sigma weight residual 1.233 1.218 0.016 1.06e-02 8.90e+03 2.19e+00 ... (remaining 5037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6685 1.90 - 3.80: 119 3.80 - 5.70: 23 5.70 - 7.60: 14 7.60 - 9.49: 5 Bond angle restraints: 6846 Sorted by residual: angle pdb=" C PRO B 566 " pdb=" CA PRO B 566 " pdb=" CB PRO B 566 " ideal model delta sigma weight residual 111.40 108.16 3.24 9.10e-01 1.21e+00 1.27e+01 angle pdb=" CB MET A 554 " pdb=" CG MET A 554 " pdb=" SD MET A 554 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" CA LEU B 802 " pdb=" CB LEU B 802 " pdb=" CG LEU B 802 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 angle pdb=" CA TYR A 712 " pdb=" CB TYR A 712 " pdb=" CG TYR A 712 " ideal model delta sigma weight residual 113.90 118.70 -4.80 1.80e+00 3.09e-01 7.12e+00 angle pdb=" CA LEU B 699 " pdb=" CB LEU B 699 " pdb=" CG LEU B 699 " ideal model delta sigma weight residual 116.30 125.01 -8.71 3.50e+00 8.16e-02 6.19e+00 ... (remaining 6841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2392 16.63 - 33.25: 338 33.25 - 49.88: 115 49.88 - 66.50: 7 66.50 - 83.13: 4 Dihedral angle restraints: 2856 sinusoidal: 1060 harmonic: 1796 Sorted by residual: dihedral pdb=" CB CYS B 485 " pdb=" SG CYS B 485 " pdb=" SG CYS B 782 " pdb=" CB CYS B 782 " ideal model delta sinusoidal sigma weight residual 93.00 129.34 -36.34 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " pdb=" SG CYS A 782 " pdb=" CB CYS A 782 " ideal model delta sinusoidal sigma weight residual 93.00 127.81 -34.81 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA ASN A 482 " pdb=" C ASN A 482 " pdb=" N PHE A 483 " pdb=" CA PHE A 483 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 649 0.057 - 0.113: 123 0.113 - 0.170: 15 0.170 - 0.226: 1 0.226 - 0.283: 2 Chirality restraints: 790 Sorted by residual: chirality pdb=" CG LEU B 797 " pdb=" CB LEU B 797 " pdb=" CD1 LEU B 797 " pdb=" CD2 LEU B 797 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU A 326 " pdb=" CB LEU A 326 " pdb=" CD1 LEU A 326 " pdb=" CD2 LEU A 326 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CG LEU A 797 " pdb=" CB LEU A 797 " pdb=" CD1 LEU A 797 " pdb=" CD2 LEU A 797 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 787 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 457 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO A 458 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 457 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 458 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 794 " 0.011 2.00e-02 2.50e+03 1.15e-02 3.29e+00 pdb=" CG TRP A 794 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 794 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 794 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 794 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 794 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 794 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 794 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 794 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 794 " -0.000 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 947 2.76 - 3.30: 5064 3.30 - 3.83: 8108 3.83 - 4.37: 8859 4.37 - 4.90: 15037 Nonbonded interactions: 38015 Sorted by model distance: nonbonded pdb=" O VAL B 469 " pdb=" OG1 THR B 473 " model vdw 2.230 3.040 nonbonded pdb=" OG SER A 644 " pdb=" OH TYR A 724 " model vdw 2.272 3.040 nonbonded pdb=" O ILE B 747 " pdb=" OG1 THR B 750 " model vdw 2.275 3.040 nonbonded pdb=" OG SER B 644 " pdb=" OH TYR B 724 " model vdw 2.286 3.040 nonbonded pdb=" O TRP A 794 " pdb=" OG SER A 798 " model vdw 2.300 3.040 ... (remaining 38010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.310 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 0.034 5046 Z= 0.157 Angle : 0.714 9.494 6854 Z= 0.370 Chirality : 0.045 0.283 790 Planarity : 0.004 0.064 816 Dihedral : 16.894 83.125 1680 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.57 % Allowed : 27.59 % Favored : 71.84 % 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: 1.26 (0.34), residues: 586 helix: 1.52 (0.22), residues: 478 sheet: None (None), residues: 0 loop : -2.29 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 518 TYR 0.025 0.001 TYR B 321 PHE 0.020 0.001 PHE A 745 TRP 0.031 0.002 TRP A 794 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5042) covalent geometry : angle 0.71398 ( 6846) SS BOND : bond 0.00032 ( 4) SS BOND : angle 0.68372 ( 8) hydrogen bonds : bond 0.10580 ( 381) hydrogen bonds : angle 5.26945 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.184 Fit side-chains REVERT: A 325 LEU cc_start: 0.8445 (tt) cc_final: 0.8109 (mt) REVERT: B 517 ARG cc_start: 0.8342 (ptt90) cc_final: 0.8136 (ptt-90) outliers start: 3 outliers final: 2 residues processed: 115 average time/residue: 0.0585 time to fit residues: 9.2875 Evaluate side-chains 105 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 794 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0000 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.5590 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.169502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127519 restraints weight = 10742.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.130747 restraints weight = 5381.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.132665 restraints weight = 3693.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.133779 restraints weight = 3022.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.134249 restraints weight = 2723.084| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5046 Z= 0.129 Angle : 0.607 11.213 6854 Z= 0.304 Chirality : 0.039 0.173 790 Planarity : 0.003 0.042 816 Dihedral : 4.466 32.232 654 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.07 % Allowed : 24.71 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.33), residues: 586 helix: 1.64 (0.22), residues: 486 sheet: None (None), residues: 0 loop : -2.83 (0.53), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 517 TYR 0.018 0.001 TYR B 321 PHE 0.012 0.001 PHE B 806 TRP 0.003 0.001 TRP A 754 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5042) covalent geometry : angle 0.60719 ( 6846) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.49678 ( 8) hydrogen bonds : bond 0.04501 ( 381) hydrogen bonds : angle 4.38741 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.168 Fit side-chains REVERT: A 455 TYR cc_start: 0.7211 (t80) cc_final: 0.6758 (t80) REVERT: B 517 ARG cc_start: 0.8355 (ptt90) cc_final: 0.8138 (ptt-90) REVERT: B 699 LEU cc_start: 0.8894 (mm) cc_final: 0.8635 (pp) REVERT: B 753 MET cc_start: 0.7716 (mmp) cc_final: 0.7497 (mmp) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.0537 time to fit residues: 8.8892 Evaluate side-chains 111 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 758 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 59.1494 > 50: distance: 2 - 19: 15.318 distance: 6 - 24: 16.518 distance: 13 - 19: 15.647 distance: 19 - 20: 24.610 distance: 20 - 21: 41.209 distance: 20 - 23: 26.173 distance: 21 - 22: 16.828 distance: 21 - 24: 16.653 distance: 24 - 25: 24.820 distance: 25 - 26: 19.670 distance: 25 - 28: 8.523 distance: 26 - 27: 22.108 distance: 26 - 32: 17.576 distance: 28 - 29: 32.214 distance: 29 - 30: 23.726 distance: 29 - 31: 9.223 distance: 32 - 33: 9.481 distance: 33 - 34: 3.262 distance: 33 - 36: 7.770 distance: 34 - 35: 14.276 distance: 36 - 37: 11.703 distance: 38 - 39: 14.052 distance: 39 - 40: 24.963 distance: 39 - 42: 25.675 distance: 40 - 41: 29.370 distance: 40 - 46: 38.252 distance: 42 - 43: 25.729 distance: 43 - 44: 11.384 distance: 44 - 45: 6.102 distance: 46 - 47: 22.728 distance: 47 - 48: 27.486 distance: 47 - 50: 6.356 distance: 48 - 49: 18.556 distance: 48 - 54: 3.283 distance: 49 - 74: 44.069 distance: 50 - 51: 6.102 distance: 51 - 52: 15.772 distance: 51 - 53: 20.147 distance: 54 - 55: 20.689 distance: 55 - 56: 21.833 distance: 55 - 58: 30.525 distance: 56 - 57: 19.164 distance: 56 - 59: 34.502 distance: 57 - 82: 41.006 distance: 59 - 60: 34.141 distance: 60 - 61: 15.494 distance: 60 - 63: 10.434 distance: 61 - 62: 18.577 distance: 61 - 67: 10.085 distance: 62 - 90: 26.924 distance: 63 - 64: 31.156 distance: 64 - 65: 18.661 distance: 65 - 66: 32.433 distance: 67 - 68: 5.027 distance: 68 - 69: 25.971 distance: 68 - 71: 24.655 distance: 69 - 70: 26.885 distance: 69 - 74: 31.808 distance: 70 - 97: 28.269 distance: 71 - 72: 39.069 distance: 71 - 73: 23.690 distance: 74 - 75: 28.569 distance: 75 - 76: 10.807 distance: 75 - 78: 4.498 distance: 76 - 77: 23.172 distance: 76 - 82: 24.168 distance: 77 - 104: 25.680 distance: 78 - 79: 10.300 distance: 79 - 80: 12.698 distance: 79 - 81: 11.574 distance: 82 - 83: 33.003 distance: 83 - 84: 10.600 distance: 83 - 86: 42.746 distance: 84 - 85: 41.808 distance: 84 - 90: 33.507 distance: 85 - 108: 13.282 distance: 86 - 87: 33.030 distance: 87 - 88: 37.769 distance: 87 - 89: 32.703