Starting phenix.real_space_refine on Sat May 10 10:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvr_27743/05_2025/8dvr_27743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvr_27743/05_2025/8dvr_27743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvr_27743/05_2025/8dvr_27743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvr_27743/05_2025/8dvr_27743.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvr_27743/05_2025/8dvr_27743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvr_27743/05_2025/8dvr_27743.cif" } resolution = 3.3 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= 0.007 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 31 5.16 5 C 3492 2.51 5 N 947 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 445 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 23.312 29.188 27.887 1.00 29.78 S ATOM 4630 SG CYS A 864 19.045 29.309 28.690 1.00 26.94 S ATOM 4669 SG CYS A 869 21.454 27.047 30.233 1.00 32.07 S Time building chain proxies: 3.82, per 1000 atoms: 0.68 Number of scatterers: 5601 At special positions: 0 Unit cell: (79.032, 99.324, 85.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 24 15.00 O 1106 8.00 N 947 7.00 C 3492 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 727.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 51.3% alpha, 8.3% beta 10 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.515A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 4.032A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.835A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.912A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.994A pdb=" N GLN A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.511A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.858A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.724A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.794A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 4.162A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.529A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 4.107A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.524A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing helix chain 'A' and resid 889 through 892 removed outlier: 3.556A pdb=" N PHE A 892 " --> pdb=" O ILE A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 7.183A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.894A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.874A pdb=" N LEU A 808 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.500A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 5.749A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.60 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: 1711 1.34 - 1.46: 902 1.46 - 1.57: 3057 1.57 - 1.69: 45 1.69 - 1.81: 43 Bond restraints: 5758 Sorted by residual: bond pdb=" C ILE A 884 " pdb=" O ILE A 884 " ideal model delta sigma weight residual 1.232 1.241 -0.009 8.90e-03 1.26e+04 9.64e-01 bond pdb=" N PRO A 401 " pdb=" CA PRO A 401 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.60e-01 bond pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.38e-01 bond pdb=" C VAL A 414 " pdb=" N GLY A 415 " ideal model delta sigma weight residual 1.331 1.319 0.011 1.46e-02 4.69e+03 5.79e-01 bond pdb=" CA ILE A 916 " pdb=" CB ILE A 916 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 4.96e-01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 7739 1.42 - 2.84: 110 2.84 - 4.27: 19 4.27 - 5.69: 3 5.69 - 7.11: 1 Bond angle restraints: 7872 Sorted by residual: angle pdb=" N ILE A 897 " pdb=" CA ILE A 897 " pdb=" C ILE A 897 " ideal model delta sigma weight residual 111.90 109.07 2.83 8.10e-01 1.52e+00 1.22e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 111.90 109.36 2.54 8.10e-01 1.52e+00 9.82e+00 angle pdb=" N ALA A 410 " pdb=" CA ALA A 410 " pdb=" C ALA A 410 " ideal model delta sigma weight residual 114.04 110.54 3.50 1.24e+00 6.50e-01 7.98e+00 angle pdb=" C2' GTP B 201 " pdb=" C3' GTP B 201 " pdb=" C4' GTP B 201 " ideal model delta sigma weight residual 111.00 103.89 7.11 3.00e+00 1.11e-01 5.62e+00 angle pdb=" N ILE A 884 " pdb=" CA ILE A 884 " pdb=" C ILE A 884 " ideal model delta sigma weight residual 107.61 110.31 -2.70 1.19e+00 7.06e-01 5.14e+00 ... (remaining 7867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3153 17.86 - 35.71: 265 35.71 - 53.57: 73 53.57 - 71.43: 29 71.43 - 89.28: 15 Dihedral angle restraints: 3535 sinusoidal: 1663 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 23.63 80.96 1 2.00e+01 2.50e-03 2.02e+01 dihedral pdb=" CA PHE A 853 " pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CB GLU A 895 " pdb=" CG GLU A 895 " pdb=" CD GLU A 895 " pdb=" OE1 GLU A 895 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 557 0.024 - 0.049: 201 0.049 - 0.073: 75 0.073 - 0.098: 43 0.098 - 0.122: 17 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 875 " pdb=" N ILE A 875 " pdb=" C ILE A 875 " pdb=" CB ILE A 875 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE A 629 " pdb=" N ILE A 629 " pdb=" C ILE A 629 " pdb=" CB ILE A 629 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 890 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.31e-01 pdb=" N PRO A 382 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 300 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.26e-01 pdb=" N PRO A 301 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 884 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.12e-01 pdb=" N PRO A 885 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 885 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 885 " 0.011 5.00e-02 4.00e+02 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1363 2.79 - 3.32: 5223 3.32 - 3.85: 9434 3.85 - 4.37: 10722 4.37 - 4.90: 18061 Nonbonded interactions: 44803 Sorted by model distance: nonbonded pdb=" ND2 ASN A 259 " pdb=" O ASP A 435 " model vdw 2.267 3.120 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.325 3.040 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR A 622 " pdb=" OD1 ASN A 692 " model vdw 2.349 3.040 nonbonded pdb=" N ASP A 580 " pdb=" OD1 ASP A 580 " model vdw 2.355 3.120 ... (remaining 44798 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.060 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.008 0.524 5762 Z= 0.288 Angle : 0.456 7.111 7872 Z= 0.269 Chirality : 0.035 0.122 893 Planarity : 0.002 0.024 924 Dihedral : 15.720 89.284 2315 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.40 % Allowed : 9.46 % Favored : 89.14 % 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: -2.25 (0.31), residues: 627 helix: 0.37 (0.28), residues: 280 sheet: -3.31 (0.51), residues: 81 loop : -3.00 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 847 PHE 0.007 0.001 PHE A 856 TYR 0.003 0.000 TYR A 390 ARG 0.001 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.12908 ( 269) hydrogen bonds : angle 5.04169 ( 764) metal coordination : bond 0.35537 ( 3) covalent geometry : bond 0.00166 ( 5758) covalent geometry : angle 0.45573 ( 7872) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 492 ASP cc_start: 0.7105 (p0) cc_final: 0.6518 (t0) REVERT: A 759 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7442 (ttpp) REVERT: A 763 ASP cc_start: 0.7733 (t70) cc_final: 0.7508 (t0) REVERT: A 789 PHE cc_start: 0.7957 (t80) cc_final: 0.7567 (t80) REVERT: A 889 ILE cc_start: 0.9123 (tp) cc_final: 0.8588 (tp) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.2297 time to fit residues: 39.0946 Evaluate side-chains 93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 499 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 341 ASN A 354 ASN A 380 GLN A 495 ASN A 517 GLN A 573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124635 restraints weight = 6363.171| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.79 r_work: 0.3360 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5762 Z= 0.132 Angle : 0.523 8.443 7872 Z= 0.258 Chirality : 0.039 0.186 893 Planarity : 0.003 0.036 924 Dihedral : 13.194 91.866 1015 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.85 % Allowed : 11.21 % Favored : 84.94 % 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: -1.16 (0.34), residues: 627 helix: 1.49 (0.30), residues: 288 sheet: -3.20 (0.48), residues: 92 loop : -2.59 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 873 HIS 0.003 0.001 HIS A 281 PHE 0.009 0.001 PHE A 371 TYR 0.012 0.001 TYR A 383 ARG 0.008 0.001 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 269) hydrogen bonds : angle 3.83244 ( 764) metal coordination : bond 0.01894 ( 3) covalent geometry : bond 0.00302 ( 5758) covalent geometry : angle 0.52333 ( 7872) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.610 Fit side-chains REVERT: A 255 MET cc_start: 0.8791 (mtt) cc_final: 0.8430 (mtt) REVERT: A 289 GLN cc_start: 0.6768 (mp10) cc_final: 0.6452 (mp10) REVERT: A 632 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 653 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 692 ASN cc_start: 0.8401 (t0) cc_final: 0.8069 (t0) REVERT: A 759 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7589 (ttpp) REVERT: A 763 ASP cc_start: 0.8348 (t70) cc_final: 0.8027 (t0) REVERT: A 872 ASP cc_start: 0.8501 (t0) cc_final: 0.8209 (t0) outliers start: 22 outliers final: 7 residues processed: 110 average time/residue: 0.2118 time to fit residues: 29.4027 Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.0040 chunk 6 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 573 ASN A 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133200 restraints weight = 6430.549| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.83 r_work: 0.3225 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5762 Z= 0.100 Angle : 0.486 7.932 7872 Z= 0.236 Chirality : 0.039 0.181 893 Planarity : 0.003 0.044 924 Dihedral : 13.215 91.682 1011 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.50 % Allowed : 15.59 % Favored : 80.91 % 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: -0.63 (0.34), residues: 627 helix: 1.93 (0.30), residues: 289 sheet: -3.01 (0.52), residues: 84 loop : -2.36 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 771 HIS 0.002 0.000 HIS A 281 PHE 0.011 0.001 PHE A 616 TYR 0.006 0.001 TYR A 879 ARG 0.006 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 269) hydrogen bonds : angle 3.62958 ( 764) metal coordination : bond 0.00115 ( 3) covalent geometry : bond 0.00222 ( 5758) covalent geometry : angle 0.48561 ( 7872) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.583 Fit side-chains REVERT: A 462 LYS cc_start: 0.8327 (tptm) cc_final: 0.8099 (tptp) REVERT: A 492 ASP cc_start: 0.7191 (m-30) cc_final: 0.5900 (t0) REVERT: A 495 ASN cc_start: 0.7670 (m-40) cc_final: 0.7436 (m110) REVERT: A 632 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 647 ILE cc_start: 0.8550 (mt) cc_final: 0.8294 (mp) REVERT: A 653 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7957 (pp) REVERT: A 759 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7550 (ttpp) REVERT: A 763 ASP cc_start: 0.8199 (t70) cc_final: 0.7884 (t0) REVERT: A 816 LEU cc_start: 0.8941 (tt) cc_final: 0.8715 (tt) outliers start: 20 outliers final: 8 residues processed: 97 average time/residue: 0.1720 time to fit residues: 22.4018 Evaluate side-chains 81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 573 ASN A 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125373 restraints weight = 6495.120| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.83 r_work: 0.3166 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5762 Z= 0.130 Angle : 0.525 8.379 7872 Z= 0.257 Chirality : 0.041 0.187 893 Planarity : 0.003 0.045 924 Dihedral : 13.201 93.915 1011 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.15 % Allowed : 17.34 % Favored : 79.51 % 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: -0.46 (0.34), residues: 627 helix: 2.07 (0.31), residues: 285 sheet: -2.87 (0.53), residues: 84 loop : -2.23 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 873 HIS 0.003 0.001 HIS A 281 PHE 0.017 0.001 PHE A 460 TYR 0.008 0.001 TYR A 566 ARG 0.009 0.001 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 269) hydrogen bonds : angle 3.66449 ( 764) metal coordination : bond 0.00182 ( 3) covalent geometry : bond 0.00301 ( 5758) covalent geometry : angle 0.52468 ( 7872) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.561 Fit side-chains REVERT: A 492 ASP cc_start: 0.7243 (m-30) cc_final: 0.5940 (t0) REVERT: A 546 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7411 (ttt90) REVERT: A 632 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8320 (tt) REVERT: A 647 ILE cc_start: 0.8670 (mt) cc_final: 0.8424 (mp) REVERT: A 653 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7845 (pp) REVERT: A 759 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7553 (ttpp) REVERT: A 763 ASP cc_start: 0.8226 (t70) cc_final: 0.7920 (t0) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 0.1739 time to fit residues: 20.4018 Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 56 optimal weight: 0.0060 chunk 54 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129158 restraints weight = 6408.660| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.86 r_work: 0.3220 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5762 Z= 0.094 Angle : 0.486 7.862 7872 Z= 0.237 Chirality : 0.039 0.162 893 Planarity : 0.003 0.042 924 Dihedral : 13.211 92.775 1011 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.80 % Allowed : 17.86 % Favored : 79.33 % 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: -0.19 (0.35), residues: 627 helix: 2.25 (0.31), residues: 287 sheet: -2.66 (0.54), residues: 79 loop : -2.12 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 771 HIS 0.002 0.000 HIS A 847 PHE 0.021 0.001 PHE A 616 TYR 0.008 0.001 TYR A 390 ARG 0.005 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 269) hydrogen bonds : angle 3.52560 ( 764) metal coordination : bond 0.00126 ( 3) covalent geometry : bond 0.00206 ( 5758) covalent geometry : angle 0.48553 ( 7872) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.626 Fit side-chains REVERT: A 492 ASP cc_start: 0.7169 (m-30) cc_final: 0.5903 (t0) REVERT: A 546 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7539 (ttt90) REVERT: A 632 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 647 ILE cc_start: 0.8721 (mt) cc_final: 0.8464 (mp) REVERT: A 653 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7864 (pp) REVERT: A 692 ASN cc_start: 0.8338 (t0) cc_final: 0.8115 (t0) REVERT: A 759 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7500 (ttpp) REVERT: A 763 ASP cc_start: 0.8239 (t70) cc_final: 0.7910 (t0) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.1629 time to fit residues: 17.9561 Evaluate side-chains 75 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129865 restraints weight = 6378.719| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.82 r_work: 0.3184 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5762 Z= 0.105 Angle : 0.483 8.132 7872 Z= 0.235 Chirality : 0.039 0.151 893 Planarity : 0.003 0.042 924 Dihedral : 13.194 93.715 1010 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.98 % Allowed : 19.26 % Favored : 77.76 % 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: -0.10 (0.35), residues: 627 helix: 2.29 (0.30), residues: 293 sheet: -2.73 (0.52), residues: 85 loop : -2.06 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 873 HIS 0.002 0.000 HIS A 847 PHE 0.019 0.001 PHE A 616 TYR 0.008 0.001 TYR A 390 ARG 0.005 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 269) hydrogen bonds : angle 3.53983 ( 764) metal coordination : bond 0.00106 ( 3) covalent geometry : bond 0.00237 ( 5758) covalent geometry : angle 0.48260 ( 7872) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.604 Fit side-chains REVERT: A 492 ASP cc_start: 0.7351 (m-30) cc_final: 0.6009 (t0) REVERT: A 546 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7638 (ttt90) REVERT: A 632 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 647 ILE cc_start: 0.8818 (mt) cc_final: 0.8554 (mp) REVERT: A 653 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7927 (pp) REVERT: A 692 ASN cc_start: 0.8448 (t0) cc_final: 0.8235 (t0) REVERT: A 759 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7592 (ttpp) REVERT: A 763 ASP cc_start: 0.8399 (t70) cc_final: 0.8101 (t0) REVERT: A 794 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6938 (pp30) outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 0.1769 time to fit residues: 20.6350 Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125284 restraints weight = 6444.904| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.00 r_work: 0.3119 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5762 Z= 0.126 Angle : 0.526 8.569 7872 Z= 0.256 Chirality : 0.040 0.211 893 Planarity : 0.003 0.038 924 Dihedral : 13.219 94.574 1010 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.50 % Allowed : 18.91 % Favored : 77.58 % 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: -0.05 (0.35), residues: 627 helix: 2.25 (0.30), residues: 294 sheet: -2.62 (0.53), residues: 85 loop : -1.97 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 873 HIS 0.001 0.000 HIS A 847 PHE 0.013 0.001 PHE A 460 TYR 0.009 0.001 TYR A 390 ARG 0.006 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 269) hydrogen bonds : angle 3.62028 ( 764) metal coordination : bond 0.00150 ( 3) covalent geometry : bond 0.00289 ( 5758) covalent geometry : angle 0.52550 ( 7872) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.594 Fit side-chains REVERT: A 492 ASP cc_start: 0.7293 (m-30) cc_final: 0.6013 (t0) REVERT: A 546 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7436 (ttt90) REVERT: A 632 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 647 ILE cc_start: 0.8775 (mt) cc_final: 0.8535 (mp) REVERT: A 653 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7954 (pp) REVERT: A 692 ASN cc_start: 0.8428 (t0) cc_final: 0.8208 (t0) REVERT: A 759 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7465 (ttpp) REVERT: A 763 ASP cc_start: 0.8261 (t70) cc_final: 0.7949 (t0) REVERT: A 794 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6960 (pp30) outliers start: 20 outliers final: 10 residues processed: 86 average time/residue: 0.1613 time to fit residues: 18.7336 Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 62.7898 > 50: distance: 22 - 134: 24.845 distance: 25 - 131: 32.249 distance: 35 - 117: 21.799 distance: 38 - 114: 22.879 distance: 82 - 89: 18.386 distance: 89 - 90: 19.426 distance: 90 - 91: 9.915 distance: 91 - 92: 10.355 distance: 91 - 98: 46.238 distance: 93 - 94: 44.813 distance: 94 - 95: 49.034 distance: 95 - 96: 45.961 distance: 96 - 97: 12.822 distance: 98 - 99: 28.194 distance: 99 - 100: 60.986 distance: 99 - 102: 12.946 distance: 100 - 101: 18.680 distance: 100 - 109: 25.188 distance: 102 - 103: 15.709 distance: 103 - 104: 44.154 distance: 104 - 105: 3.801 distance: 105 - 106: 18.711 distance: 106 - 107: 11.031 distance: 106 - 108: 12.452 distance: 109 - 110: 17.427 distance: 109 - 232: 18.412 distance: 110 - 111: 18.689 distance: 110 - 113: 23.819 distance: 111 - 112: 25.605 distance: 111 - 114: 16.249 distance: 112 - 229: 24.569 distance: 114 - 115: 15.308 distance: 115 - 116: 28.808 distance: 115 - 118: 30.256 distance: 116 - 117: 15.859 distance: 116 - 123: 13.433 distance: 118 - 119: 54.287 distance: 119 - 120: 19.179 distance: 120 - 121: 37.194 distance: 121 - 122: 38.179 distance: 123 - 124: 27.800 distance: 124 - 125: 29.239 distance: 124 - 127: 14.584 distance: 125 - 126: 15.373 distance: 125 - 131: 39.379 distance: 127 - 128: 39.733 distance: 127 - 129: 42.071 distance: 128 - 130: 62.273 distance: 131 - 132: 12.137 distance: 132 - 133: 15.157 distance: 132 - 135: 21.926 distance: 133 - 134: 15.804 distance: 133 - 142: 43.155 distance: 135 - 136: 48.880 distance: 136 - 137: 12.310 distance: 136 - 138: 4.789 distance: 137 - 139: 51.156 distance: 138 - 140: 32.374 distance: 139 - 141: 24.816 distance: 140 - 141: 31.750 distance: 142 - 143: 21.284 distance: 143 - 144: 18.012 distance: 143 - 146: 32.972 distance: 144 - 145: 33.620 distance: 144 - 148: 48.912 distance: 146 - 147: 62.790 distance: 147 - 258: 33.659 distance: 148 - 149: 28.002 distance: 149 - 150: 17.781 distance: 149 - 152: 21.001 distance: 150 - 151: 13.354 distance: 150 - 153: 17.105 distance: 153 - 154: 16.285 distance: 154 - 155: 48.579 distance: 154 - 157: 11.650 distance: 155 - 156: 51.754 distance: 155 - 164: 42.551 distance: 157 - 158: 42.020 distance: 158 - 159: 36.214 distance: 159 - 160: 33.879 distance: 160 - 161: 8.969 distance: 161 - 162: 30.424 distance: 161 - 163: 25.129 distance: 164 - 165: 15.530 distance: 165 - 166: 23.996 distance: 165 - 168: 30.208 distance: 166 - 167: 16.570 distance: 166 - 173: 17.055 distance: 168 - 169: 36.116 distance: 169 - 170: 20.214 distance: 170 - 171: 3.838 distance: 170 - 172: 16.500