Starting phenix.real_space_refine on Thu Jun 5 10:13:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2a_27830/06_2025/8e2a_27830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2a_27830/06_2025/8e2a_27830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2a_27830/06_2025/8e2a_27830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2a_27830/06_2025/8e2a_27830.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2a_27830/06_2025/8e2a_27830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2a_27830/06_2025/8e2a_27830.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.021 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 31 5.16 5 C 3621 2.51 5 N 985 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5768 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5456 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 40, 'TRANS': 645} Chain breaks: 2 Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain breaks: 1 Time building chain proxies: 4.47, per 1000 atoms: 0.77 Number of scatterers: 5768 At special positions: 0 Unit cell: (70.35, 84.42, 109.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 15 15.00 O 1116 8.00 N 985 7.00 C 3621 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: 1.44 Conformation dependent library (CDL) restraints added in 823.9 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 9 sheets defined 32.9% alpha, 22.9% beta 4 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.730A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.664A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 3.712A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.587A pdb=" N GLN A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 500 " --> pdb=" O HIS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.666A pdb=" N ALA A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 601 removed outlier: 3.671A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 3.775A pdb=" N LEU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 651 through 666 removed outlier: 3.800A pdb=" N LEU A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.519A pdb=" N PHE A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.817A pdb=" N VAL A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 766 removed outlier: 3.646A pdb=" N THR A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.335A pdb=" N LEU A 110 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE A 238 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 112 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.954A pdb=" N GLY A 569 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLN A 568 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 302 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 4.012A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 383 removed outlier: 6.157A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA8, first strand: chain 'A' and resid 791 through 796 removed outlier: 3.636A pdb=" N VAL A 791 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP A 783 " --> pdb=" O MET A 775 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 810 238 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1662 1.33 - 1.45: 928 1.45 - 1.57: 3253 1.57 - 1.69: 28 1.69 - 1.81: 47 Bond restraints: 5918 Sorted by residual: bond pdb=" C ARG A 616 " pdb=" O ARG A 616 " ideal model delta sigma weight residual 1.235 1.217 0.019 1.26e-02 6.30e+03 2.16e+00 bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" CA GLY A 811 " pdb=" C GLY A 811 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.21e+00 bond pdb=" CG LEU A 423 " pdb=" CD1 LEU A 423 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" C ARG A 616 " pdb=" N MET A 617 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.35e-02 5.49e+03 1.10e+00 ... (remaining 5913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 7782 1.62 - 3.24: 234 3.24 - 4.86: 46 4.86 - 6.48: 8 6.48 - 8.10: 4 Bond angle restraints: 8074 Sorted by residual: angle pdb=" C LYS A 812 " pdb=" N LYS A 813 " pdb=" CA LYS A 813 " ideal model delta sigma weight residual 121.61 126.86 -5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" N MET A 617 " pdb=" CA MET A 617 " pdb=" C MET A 617 " ideal model delta sigma weight residual 112.38 116.17 -3.79 1.22e+00 6.72e-01 9.65e+00 angle pdb=" C ARG A 616 " pdb=" CA ARG A 616 " pdb=" CB ARG A 616 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 angle pdb=" C THR A 615 " pdb=" N ARG A 616 " pdb=" CA ARG A 616 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" N SER A 848 " pdb=" CA SER A 848 " pdb=" C SER A 848 " ideal model delta sigma weight residual 111.02 114.01 -2.99 1.22e+00 6.72e-01 5.99e+00 ... (remaining 8069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3336 17.71 - 35.42: 243 35.42 - 53.13: 45 53.13 - 70.83: 28 70.83 - 88.54: 11 Dihedral angle restraints: 3663 sinusoidal: 1651 harmonic: 2012 Sorted by residual: dihedral pdb=" CA ASP A 824 " pdb=" C ASP A 824 " pdb=" N MET A 825 " pdb=" CA MET A 825 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N TYR A 674 " pdb=" CA TYR A 674 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE A 699 " pdb=" C PHE A 699 " pdb=" N THR A 700 " pdb=" CA THR A 700 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 3660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 764 0.062 - 0.124: 145 0.124 - 0.186: 13 0.186 - 0.248: 0 0.248 - 0.310: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" CG LEU A 618 " pdb=" CB LEU A 618 " pdb=" CD1 LEU A 618 " pdb=" CD2 LEU A 618 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ARG A 616 " pdb=" N ARG A 616 " pdb=" C ARG A 616 " pdb=" CB ARG A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA HIS A 409 " pdb=" N HIS A 409 " pdb=" C HIS A 409 " pdb=" CB HIS A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 920 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 610 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 611 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 634 " 0.013 2.00e-02 2.50e+03 1.09e-02 2.09e+00 pdb=" CG PHE A 634 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 634 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 634 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 634 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 634 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 634 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 648 " 0.007 2.00e-02 2.50e+03 1.07e-02 2.00e+00 pdb=" CG PHE A 648 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 648 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 648 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 648 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 648 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 648 " -0.000 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 226 2.72 - 3.26: 5283 3.26 - 3.81: 8564 3.81 - 4.35: 11167 4.35 - 4.90: 19247 Nonbonded interactions: 44487 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.173 3.040 nonbonded pdb=" OD1 ASP A 651 " pdb=" N LYS A 652 " model vdw 2.182 3.120 nonbonded pdb=" ND1 HIS A 409 " pdb=" OG SER A 465 " model vdw 2.249 3.120 nonbonded pdb=" OD2 ASP A 307 " pdb=" NZ LYS A 309 " model vdw 2.283 3.120 nonbonded pdb=" OD2 ASP A 412 " pdb=" NH1 ARG A 483 " model vdw 2.314 3.120 ... (remaining 44482 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.004 0.038 5918 Z= 0.185 Angle : 0.709 8.103 8074 Z= 0.379 Chirality : 0.047 0.310 923 Planarity : 0.005 0.048 990 Dihedral : 14.471 88.543 2353 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.31), residues: 680 helix: 1.18 (0.36), residues: 208 sheet: 0.34 (0.38), residues: 161 loop : -1.32 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.005 0.001 HIS A 409 PHE 0.025 0.002 PHE A 634 TYR 0.018 0.002 TYR A 853 ARG 0.007 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.10103 ( 250) hydrogen bonds : angle 5.39520 ( 687) covalent geometry : bond 0.00428 ( 5918) covalent geometry : angle 0.70874 ( 8074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.630 Fit side-chains REVERT: A 54 MET cc_start: 0.6703 (tpt) cc_final: 0.6386 (tpp) REVERT: A 74 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6557 (ttp-110) REVERT: A 242 LYS cc_start: 0.7942 (mttt) cc_final: 0.7730 (mmtm) REVERT: A 318 GLN cc_start: 0.7127 (tt0) cc_final: 0.6890 (mt0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.5634 time to fit residues: 150.8805 Evaluate side-chains 55 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113573 restraints weight = 6217.977| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.30 r_work: 0.3267 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5918 Z= 0.123 Angle : 0.579 9.721 8074 Z= 0.290 Chirality : 0.042 0.138 923 Planarity : 0.004 0.040 990 Dihedral : 12.327 73.054 985 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.49 % Allowed : 8.46 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.32), residues: 680 helix: 1.66 (0.37), residues: 209 sheet: 0.24 (0.38), residues: 170 loop : -1.11 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 243 PHE 0.013 0.002 PHE A 648 TYR 0.010 0.001 TYR A 674 ARG 0.005 0.000 ARG A 803 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 250) hydrogen bonds : angle 4.27507 ( 687) covalent geometry : bond 0.00282 ( 5918) covalent geometry : angle 0.57862 ( 8074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.7477 (tt0) cc_final: 0.7130 (mt0) REVERT: A 681 GLN cc_start: 0.7409 (mm110) cc_final: 0.7170 (mm110) REVERT: A 841 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6878 (mt-10) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 1.2918 time to fit residues: 89.3469 Evaluate side-chains 58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111690 restraints weight = 6263.961| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.27 r_work: 0.3248 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5918 Z= 0.144 Angle : 0.577 8.518 8074 Z= 0.286 Chirality : 0.043 0.140 923 Planarity : 0.004 0.043 990 Dihedral : 12.114 73.154 985 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.66 % Allowed : 10.45 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.32), residues: 680 helix: 1.91 (0.37), residues: 203 sheet: 0.36 (0.38), residues: 170 loop : -1.11 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 PHE 0.013 0.002 PHE A 757 TYR 0.009 0.001 TYR A 674 ARG 0.004 0.000 ARG A 803 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 250) hydrogen bonds : angle 4.15276 ( 687) covalent geometry : bond 0.00343 ( 5918) covalent geometry : angle 0.57739 ( 8074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.7473 (tt0) cc_final: 0.7111 (mt0) REVERT: A 523 GLU cc_start: 0.7442 (mp0) cc_final: 0.6662 (mm-30) REVERT: A 841 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6855 (mt-10) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 2.3028 time to fit residues: 133.1942 Evaluate side-chains 57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.152351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110436 restraints weight = 6296.007| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.31 r_work: 0.3208 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5918 Z= 0.130 Angle : 0.547 7.913 8074 Z= 0.273 Chirality : 0.042 0.139 923 Planarity : 0.004 0.040 990 Dihedral : 11.961 73.170 985 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.33 % Allowed : 11.44 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.32), residues: 680 helix: 1.99 (0.37), residues: 205 sheet: 0.36 (0.39), residues: 170 loop : -1.05 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 PHE 0.014 0.002 PHE A 80 TYR 0.008 0.001 TYR A 674 ARG 0.006 0.000 ARG A 803 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 250) hydrogen bonds : angle 4.02244 ( 687) covalent geometry : bond 0.00307 ( 5918) covalent geometry : angle 0.54678 ( 8074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.617 Fit side-chains REVERT: A 318 GLN cc_start: 0.7436 (tt0) cc_final: 0.7075 (mt0) REVERT: A 523 GLU cc_start: 0.7394 (mp0) cc_final: 0.6578 (mm-30) REVERT: A 841 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6856 (mt-10) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 1.6846 time to fit residues: 102.0254 Evaluate side-chains 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 68 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112742 restraints weight = 6188.280| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.37 r_work: 0.3244 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5918 Z= 0.100 Angle : 0.510 8.680 8074 Z= 0.255 Chirality : 0.041 0.135 923 Planarity : 0.004 0.035 990 Dihedral : 11.837 73.173 985 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.16 % Allowed : 11.94 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 680 helix: 2.25 (0.37), residues: 205 sheet: 0.32 (0.38), residues: 170 loop : -0.89 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 PHE 0.016 0.001 PHE A 80 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 803 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 250) hydrogen bonds : angle 3.82468 ( 687) covalent geometry : bond 0.00224 ( 5918) covalent geometry : angle 0.50971 ( 8074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.625 Fit side-chains REVERT: A 54 MET cc_start: 0.7045 (mmm) cc_final: 0.6606 (tpt) REVERT: A 318 GLN cc_start: 0.7393 (tt0) cc_final: 0.7054 (mt0) REVERT: A 523 GLU cc_start: 0.7350 (mp0) cc_final: 0.6510 (mm-30) REVERT: A 841 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6849 (mt-10) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 1.3802 time to fit residues: 87.9659 Evaluate side-chains 57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 681 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112807 restraints weight = 6219.006| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.38 r_work: 0.3244 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5918 Z= 0.100 Angle : 0.502 6.714 8074 Z= 0.252 Chirality : 0.041 0.135 923 Planarity : 0.004 0.032 990 Dihedral : 11.757 73.152 985 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.49 % Allowed : 12.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.33), residues: 680 helix: 2.21 (0.37), residues: 211 sheet: 0.40 (0.38), residues: 170 loop : -0.85 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 PHE 0.016 0.001 PHE A 80 TYR 0.008 0.001 TYR A 674 ARG 0.003 0.000 ARG A 803 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 250) hydrogen bonds : angle 3.76701 ( 687) covalent geometry : bond 0.00225 ( 5918) covalent geometry : angle 0.50153 ( 8074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7008 (mmm) cc_final: 0.6596 (tpt) REVERT: A 318 GLN cc_start: 0.7376 (tt0) cc_final: 0.7018 (mt0) REVERT: A 523 GLU cc_start: 0.7342 (mp0) cc_final: 0.6498 (mm-30) REVERT: A 681 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7686 (mm110) REVERT: A 841 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6842 (mt-10) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 1.3928 time to fit residues: 91.6832 Evaluate side-chains 56 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5884 > 50: distance: 18 - 108: 35.725 distance: 21 - 105: 34.012 distance: 47 - 52: 33.954 distance: 52 - 53: 55.218 distance: 53 - 54: 35.772 distance: 53 - 56: 5.784 distance: 54 - 61: 68.470 distance: 56 - 57: 36.478 distance: 57 - 58: 39.888 distance: 59 - 60: 16.161 distance: 62 - 65: 39.749 distance: 63 - 64: 40.349 distance: 63 - 70: 40.696 distance: 67 - 68: 39.571 distance: 70 - 71: 44.121 distance: 71 - 72: 20.259 distance: 71 - 74: 20.734 distance: 76 - 78: 39.959 distance: 77 - 79: 39.925 distance: 82 - 85: 39.614 distance: 83 - 84: 56.161 distance: 83 - 91: 57.429 distance: 85 - 86: 39.468 distance: 86 - 87: 70.082 distance: 86 - 88: 40.086 distance: 87 - 89: 33.815 distance: 89 - 90: 66.148 distance: 91 - 92: 39.103 distance: 92 - 95: 40.696 distance: 93 - 100: 38.867 distance: 95 - 96: 39.150 distance: 97 - 98: 40.000 distance: 100 - 189: 31.551 distance: 101 - 102: 39.302 distance: 101 - 104: 39.300 distance: 102 - 103: 40.701 distance: 103 - 186: 32.801 distance: 105 - 106: 39.342 distance: 107 - 116: 40.186 distance: 109 - 110: 40.535 distance: 116 - 170: 36.150 distance: 118 - 124: 39.343 distance: 119 - 167: 36.226 distance: 120 - 121: 31.376 distance: 120 - 122: 41.041 distance: 121 - 123: 32.847 distance: 124 - 130: 38.820 distance: 128 - 129: 39.540 distance: 131 - 132: 57.294 distance: 132 - 135: 40.516 distance: 133 - 134: 56.858 distance: 133 - 137: 33.605