Starting phenix.real_space_refine on Fri May 16 11:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lys_23600/05_2025/7lys_23600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lys_23600/05_2025/7lys_23600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lys_23600/05_2025/7lys_23600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lys_23600/05_2025/7lys_23600.map" model { file = "/net/cci-nas-00/data/ceres_data/7lys_23600/05_2025/7lys_23600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lys_23600/05_2025/7lys_23600.cif" } resolution = 3.05 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= 0.171 sd= 1.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 899 atoms to isotropic. 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 P 88 5.49 5 S 14 5.16 5 C 4232 2.51 5 N 1313 2.21 5 O 1552 1.98 5 H 6374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10734 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 39, 'TRANS': 629} Chain breaks: 2 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1323 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 948 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 7.40, per 1000 atoms: 0.55 Number of scatterers: 13573 At special positions: 0 Unit cell: (84.74, 99.235, 125.995, 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) S 14 16.00 P 88 15.00 O 1552 8.00 N 1313 7.00 C 4232 6.00 H 6374 1.00 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: 3.98 Conformation dependent library (CDL) restraints added in 957.6 milliseconds 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.7% alpha, 9.4% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 40 through 48 removed outlier: 4.311A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.648A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.740A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.194A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.838A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 483 removed outlier: 5.461A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 568 through 597 removed outlier: 3.531A pdb=" N LYS A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.347A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.741A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.313A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 391 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 606 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU A 395 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 388 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.562A pdb=" N VAL A 533 " --> pdb=" O PHE A 517 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6365 1.03 - 1.23: 51 1.23 - 1.42: 3348 1.42 - 1.62: 4126 1.62 - 1.81: 19 Bond restraints: 13909 Sorted by residual: bond pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" O4' DC C 3 " pdb=" C1' DC C 3 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.65e-01 bond pdb=" O4' DT D -5 " pdb=" C1' DT D -5 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.57e-01 bond pdb=" CB ARG A 488 " pdb=" CG ARG A 488 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.15e-01 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 21788 0.83 - 1.66: 2786 1.66 - 2.48: 432 2.48 - 3.31: 127 3.31 - 4.14: 14 Bond angle restraints: 25147 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 105.07 -3.47 1.50e+00 4.44e-01 5.35e+00 angle pdb=" C3' DC D 5 " pdb=" C2' DC D 5 " pdb=" C1' DC D 5 " ideal model delta sigma weight residual 101.60 104.72 -3.12 1.50e+00 4.44e-01 4.33e+00 angle pdb=" C4' DC D -9 " pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 110.00 113.04 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 102.40 105.03 -2.63 1.50e+00 4.44e-01 3.08e+00 angle pdb=" C3' DT C -8 " pdb=" C2' DT C -8 " pdb=" C1' DT C -8 " ideal model delta sigma weight residual 101.60 104.10 -2.50 1.50e+00 4.44e-01 2.79e+00 ... (remaining 25142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 5952 33.78 - 67.57: 436 67.57 - 101.35: 20 101.35 - 135.13: 0 135.13 - 168.92: 2 Dihedral angle restraints: 6410 sinusoidal: 4152 harmonic: 2258 Sorted by residual: dihedral pdb=" CA PRO A 171 " pdb=" C PRO A 171 " pdb=" N GLU A 172 " pdb=" CA GLU A 172 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 236 " pdb=" C VAL A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE A 653 " pdb=" C PHE A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 779 0.029 - 0.058: 297 0.058 - 0.087: 62 0.087 - 0.117: 61 0.117 - 0.146: 8 Chirality restraints: 1207 Sorted by residual: chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 302 " pdb=" N VAL A 302 " pdb=" C VAL A 302 " pdb=" CB VAL A 302 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1204 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 620 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 621 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 60 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 61 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 614 " 0.007 2.00e-02 2.50e+03 6.11e-03 8.39e-01 pdb=" CG HIS A 614 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 614 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 614 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS A 614 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 614 " -0.001 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 815 2.20 - 2.80: 25702 2.80 - 3.40: 35520 3.40 - 4.00: 47770 4.00 - 4.60: 71518 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLU A 184 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLN A 386 " pdb=" H GLN A 386 " model vdw 1.625 2.450 nonbonded pdb="HH12 ARG A 582 " pdb=" OP2 G B 2 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS A 536 " pdb=" O5' DG C -18 " model vdw 1.636 2.450 nonbonded pdb=" HH TYR A 123 " pdb=" OH TYR A 201 " model vdw 1.679 2.450 ... (remaining 181320 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.230 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7535 Z= 0.163 Angle : 0.540 4.141 10601 Z= 0.315 Chirality : 0.038 0.146 1207 Planarity : 0.003 0.032 1048 Dihedral : 20.021 168.916 3244 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % 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: -1.46 (0.30), residues: 663 helix: -0.22 (0.29), residues: 295 sheet: -1.50 (0.55), residues: 74 loop : -1.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.015 0.001 PHE A 613 TYR 0.010 0.001 TYR A 201 ARG 0.004 0.001 ARG A 538 Details of bonding type rmsd hydrogen bonds : bond 0.21570 ( 344) hydrogen bonds : angle 7.08980 ( 910) covalent geometry : bond 0.00344 ( 7535) covalent geometry : angle 0.54014 (10601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9280 (mm) cc_final: 0.9040 (mt) REVERT: A 659 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8245 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.5333 time to fit residues: 62.7432 Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.076330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066608 restraints weight = 43382.392| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.69 r_work: 0.2844 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7535 Z= 0.159 Angle : 0.565 3.864 10601 Z= 0.319 Chirality : 0.039 0.150 1207 Planarity : 0.004 0.036 1048 Dihedral : 21.683 168.852 1908 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % 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: -0.34 (0.32), residues: 663 helix: 0.82 (0.30), residues: 303 sheet: -1.33 (0.58), residues: 74 loop : -1.00 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.018 0.001 PHE A 613 TYR 0.008 0.001 TYR A 654 ARG 0.004 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 344) hydrogen bonds : angle 4.73138 ( 910) covalent geometry : bond 0.00333 ( 7535) covalent geometry : angle 0.56450 (10601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8307 (mtt-85) REVERT: A 659 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8258 (mtt-85) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.6345 time to fit residues: 62.5865 Evaluate side-chains 70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.076824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.067074 restraints weight = 43986.490| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.70 r_work: 0.2852 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7535 Z= 0.138 Angle : 0.532 4.639 10601 Z= 0.298 Chirality : 0.038 0.141 1207 Planarity : 0.004 0.050 1048 Dihedral : 21.614 170.986 1908 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.35 % Allowed : 10.82 % Favored : 88.83 % 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: 0.12 (0.33), residues: 663 helix: 1.34 (0.31), residues: 305 sheet: -1.59 (0.56), residues: 79 loop : -0.77 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.015 0.001 PHE A 354 TYR 0.009 0.001 TYR A 654 ARG 0.005 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 344) hydrogen bonds : angle 4.35371 ( 910) covalent geometry : bond 0.00296 ( 7535) covalent geometry : angle 0.53227 (10601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8675 (ttm170) cc_final: 0.8391 (mtt-85) REVERT: A 659 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8269 (mtt-85) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.6370 time to fit residues: 58.0460 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.076343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066716 restraints weight = 43372.802| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.68 r_work: 0.2847 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7535 Z= 0.183 Angle : 0.542 4.818 10601 Z= 0.303 Chirality : 0.040 0.138 1207 Planarity : 0.004 0.035 1048 Dihedral : 21.563 170.129 1908 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.87 % Allowed : 12.74 % Favored : 86.39 % 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: 0.36 (0.34), residues: 663 helix: 1.57 (0.31), residues: 306 sheet: -1.49 (0.57), residues: 74 loop : -0.72 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.016 0.001 PHE A 354 TYR 0.009 0.001 TYR A 654 ARG 0.006 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 344) hydrogen bonds : angle 4.18546 ( 910) covalent geometry : bond 0.00394 ( 7535) covalent geometry : angle 0.54181 (10601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 204 ILE cc_start: 0.8394 (mm) cc_final: 0.7940 (pt) REVERT: A 284 ARG cc_start: 0.8748 (ttm170) cc_final: 0.8454 (mtt-85) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.6036 time to fit residues: 60.6294 Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.076530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.066882 restraints weight = 43371.157| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.66 r_work: 0.2848 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7535 Z= 0.163 Angle : 0.530 5.359 10601 Z= 0.296 Chirality : 0.039 0.141 1207 Planarity : 0.004 0.053 1048 Dihedral : 21.533 169.972 1908 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 13.26 % Favored : 85.69 % 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: 0.48 (0.34), residues: 663 helix: 1.71 (0.31), residues: 306 sheet: -1.69 (0.54), residues: 74 loop : -0.62 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.014 0.001 PHE A 354 TYR 0.009 0.001 TYR A 654 ARG 0.005 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 344) hydrogen bonds : angle 4.06926 ( 910) covalent geometry : bond 0.00349 ( 7535) covalent geometry : angle 0.52973 (10601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 204 ILE cc_start: 0.8386 (mm) cc_final: 0.7966 (pt) REVERT: A 284 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8426 (mtt-85) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.6255 time to fit residues: 61.9687 Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.074610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.065024 restraints weight = 43898.724| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.67 r_work: 0.2812 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7535 Z= 0.232 Angle : 0.564 4.219 10601 Z= 0.315 Chirality : 0.041 0.140 1207 Planarity : 0.005 0.035 1048 Dihedral : 21.554 169.293 1908 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.40 % Allowed : 12.91 % Favored : 85.69 % 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: 0.43 (0.34), residues: 663 helix: 1.73 (0.31), residues: 305 sheet: -1.84 (0.54), residues: 74 loop : -0.68 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 PHE 0.015 0.001 PHE A 613 TYR 0.011 0.001 TYR A 654 ARG 0.005 0.001 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 344) hydrogen bonds : angle 4.08789 ( 910) covalent geometry : bond 0.00498 ( 7535) covalent geometry : angle 0.56364 (10601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 204 ILE cc_start: 0.8514 (mm) cc_final: 0.8123 (pt) REVERT: A 284 ARG cc_start: 0.8750 (ttm170) cc_final: 0.8431 (mtt-85) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.6084 time to fit residues: 58.0909 Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.076082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.066520 restraints weight = 43187.655| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.64 r_work: 0.2842 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7535 Z= 0.150 Angle : 0.527 4.241 10601 Z= 0.295 Chirality : 0.039 0.138 1207 Planarity : 0.004 0.036 1048 Dihedral : 21.517 169.558 1908 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 13.44 % Favored : 85.51 % 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: 0.64 (0.34), residues: 663 helix: 1.87 (0.31), residues: 305 sheet: -1.47 (0.57), residues: 64 loop : -0.65 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 PHE 0.014 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.006 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 344) hydrogen bonds : angle 3.99892 ( 910) covalent geometry : bond 0.00322 ( 7535) covalent geometry : angle 0.52732 (10601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8399 (mm) cc_final: 0.8037 (pt) REVERT: A 284 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8389 (mtt-85) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.5845 time to fit residues: 54.8651 Evaluate side-chains 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER 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: 69.433 > 50: distance: 71 - 83: 20.167 distance: 83 - 84: 22.147 distance: 83 - 91: 19.804 distance: 84 - 85: 10.376 distance: 84 - 87: 14.047 distance: 84 - 92: 54.236 distance: 85 - 86: 44.269 distance: 85 - 102: 35.116 distance: 87 - 88: 15.110 distance: 87 - 89: 13.788 distance: 87 - 93: 49.134 distance: 88 - 90: 27.515 distance: 88 - 94: 12.180 distance: 88 - 95: 22.199 distance: 89 - 96: 19.838 distance: 89 - 97: 16.051 distance: 89 - 98: 18.557 distance: 90 - 99: 16.342 distance: 90 - 100: 22.719 distance: 90 - 101: 12.302 distance: 102 - 103: 15.061 distance: 102 - 109: 20.312 distance: 103 - 104: 40.217 distance: 103 - 106: 14.342 distance: 103 - 110: 37.529 distance: 104 - 105: 39.938 distance: 104 - 118: 11.545 distance: 106 - 107: 39.243 distance: 106 - 108: 38.499 distance: 106 - 111: 47.419 distance: 107 - 112: 22.918 distance: 107 - 113: 13.729 distance: 107 - 114: 15.712 distance: 108 - 115: 14.396 distance: 108 - 116: 8.470 distance: 108 - 117: 13.949 distance: 118 - 119: 23.193 distance: 118 - 126: 52.529 distance: 119 - 120: 41.110 distance: 119 - 122: 52.893 distance: 119 - 127: 34.147 distance: 120 - 121: 33.829 distance: 120 - 137: 39.097 distance: 122 - 123: 58.363 distance: 122 - 128: 56.889 distance: 122 - 129: 41.455 distance: 123 - 124: 31.503 distance: 123 - 125: 22.783 distance: 123 - 130: 21.528 distance: 124 - 131: 16.018 distance: 124 - 132: 16.073 distance: 124 - 133: 16.175 distance: 125 - 134: 5.661 distance: 125 - 135: 4.222 distance: 125 - 136: 8.988 distance: 137 - 138: 45.382 distance: 137 - 143: 61.286 distance: 138 - 139: 42.124 distance: 138 - 141: 38.412 distance: 138 - 144: 28.252 distance: 139 - 140: 54.312 distance: 139 - 151: 41.068 distance: 141 - 142: 40.845 distance: 141 - 145: 35.689 distance: 141 - 146: 45.018 distance: 142 - 143: 40.035 distance: 142 - 147: 19.659 distance: 142 - 148: 10.605 distance: 143 - 149: 56.295 distance: 143 - 150: 13.811 distance: 151 - 152: 44.762 distance: 151 - 157: 39.032 distance: 152 - 153: 43.981 distance: 152 - 155: 19.282 distance: 152 - 158: 30.248 distance: 155 - 156: 18.836 distance: 155 - 159: 26.396 distance: 155 - 160: 40.454 distance: 156 - 157: 38.441 distance: 156 - 161: 13.705 distance: 156 - 162: 29.777 distance: 157 - 163: 6.576 distance: 157 - 164: 56.641 distance: 165 - 166: 40.673 distance: 165 - 174: 39.546 distance: 166 - 167: 30.797 distance: 166 - 169: 55.343 distance: 166 - 175: 45.766 distance: 167 - 168: 43.004 distance: 167 - 180: 40.753 distance: 169 - 170: 12.447 distance: 169 - 176: 13.416 distance: 169 - 177: 33.535 distance: 170 - 171: 28.104 distance: 170 - 178: 39.350 distance: 170 - 179: 44.491 distance: 171 - 172: 16.131 distance: 171 - 173: 27.991 distance: 180 - 181: 56.706 distance: 180 - 192: 35.949 distance: 181 - 182: 19.676 distance: 181 - 184: 14.322 distance: 181 - 193: 7.916 distance: 182 - 183: 27.452 distance: 182 - 201: 21.193 distance: 184 - 185: 47.848 distance: 184 - 194: 26.265 distance: 184 - 195: 18.745 distance: 185 - 186: 39.907 distance: 185 - 187: 36.423 distance: 186 - 188: 11.940 distance: 186 - 196: 5.818 distance: 187 - 189: 18.361 distance: 187 - 197: 31.488 distance: 188 - 190: 9.795 distance: 188 - 198: 9.317 distance: 189 - 190: 7.907 distance: 189 - 199: 12.957 distance: 190 - 191: 11.140 distance: 191 - 200: 15.243 distance: 201 - 202: 47.147 distance: 201 - 206: 44.850 distance: 202 - 203: 12.578 distance: 202 - 205: 7.509 distance: 202 - 207: 25.139 distance: 203 - 204: 36.905 distance: 203 - 211: 45.184 distance: 205 - 208: 25.221 distance: 205 - 209: 38.105 distance: 205 - 210: 29.531 distance: 211 - 212: 48.793 distance: 211 - 215: 9.955 distance: 212 - 213: 21.792 distance: 212 - 216: 41.336 distance: 212 - 217: 41.325 distance: 213 - 214: 29.685 distance: 213 - 218: 24.405 distance: 218 - 219: 26.296 distance: 218 - 230: 27.975 distance: 219 - 220: 36.747 distance: 219 - 222: 30.026 distance: 219 - 231: 23.417 distance: 220 - 221: 35.702 distance: 220 - 239: 21.672 distance: 222 - 223: 27.763 distance: 222 - 232: 7.307 distance: 222 - 233: 40.771 distance: 223 - 224: 14.330 distance: 223 - 225: 17.418 distance: 224 - 226: 17.135 distance: 224 - 234: 10.361 distance: 225 - 227: 49.118 distance: 225 - 235: 42.448 distance: 226 - 228: 13.543 distance: 226 - 236: 20.185 distance: 227 - 228: 3.797 distance: 228 - 229: 4.656 distance: 229 - 238: 33.575