Starting phenix.real_space_refine on Tue Mar 11 16:30:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8z_33061/03_2025/7x8z_33061_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8z_33061/03_2025/7x8z_33061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2025/7x8z_33061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2025/7x8z_33061.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2025/7x8z_33061_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8z_33061/03_2025/7x8z_33061_trim.cif" } resolution = 4.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2114 2.51 5 N 555 2.21 5 O 647 1.98 5 H 3147 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6480 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1789 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1689 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.27, per 1000 atoms: 0.66 Number of scatterers: 6480 At special positions: 0 Unit cell: (82.071, 84.558, 75.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 647 8.00 N 555 7.00 C 2114 6.00 H 3147 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 761.0 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 8.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.623A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.077A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.950A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.950A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.459A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.852A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.588A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.780A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.580A pdb=" N THR L 59 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS L 96 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 103 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.580A pdb=" N THR L 59 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 2.33 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: 3146 1.03 - 1.23: 3 1.23 - 1.42: 1529 1.42 - 1.62: 1867 1.62 - 1.81: 21 Bond restraints: 6566 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" N GLU H 1 " pdb=" H GLU H 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 6561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 10795 1.00 - 1.99: 866 1.99 - 2.99: 75 2.99 - 3.98: 14 3.98 - 4.98: 5 Bond angle restraints: 11755 Sorted by residual: angle pdb=" C TRP L 56 " pdb=" N ALA L 57 " pdb=" CA ALA L 57 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.74e+00 angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 106.55 109.94 -3.39 1.45e+00 4.76e-01 5.48e+00 angle pdb=" CA VAL H 48 " pdb=" C VAL H 48 " pdb=" N SER H 49 " ideal model delta sigma weight residual 116.60 119.90 -3.30 1.45e+00 4.76e-01 5.18e+00 angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 109.34 114.00 -4.66 2.08e+00 2.31e-01 5.01e+00 angle pdb=" N PRO L 101 " pdb=" CA PRO L 101 " pdb=" C PRO L 101 " ideal model delta sigma weight residual 110.70 112.76 -2.06 1.22e+00 6.72e-01 2.84e+00 ... (remaining 11750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2789 15.96 - 31.92: 272 31.92 - 47.87: 90 47.87 - 63.83: 36 63.83 - 79.79: 5 Dihedral angle restraints: 3192 sinusoidal: 1689 harmonic: 1503 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 167.77 -74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 6.33 72.67 1 2.00e+01 2.50e-03 1.69e+01 dihedral pdb=" CA PHE H 27 " pdb=" C PHE H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 254 0.027 - 0.053: 150 0.053 - 0.080: 50 0.080 - 0.107: 23 0.107 - 0.133: 15 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 100 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO L 101 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 101 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 101 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO L 65 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " -0.019 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 853 2.24 - 2.83: 13946 2.83 - 3.42: 15347 3.42 - 4.01: 21243 4.01 - 4.60: 31822 Nonbonded interactions: 83211 Sorted by model distance: nonbonded pdb=" O SER A 366 " pdb="HD22 ASN A 370 " model vdw 1.650 2.450 nonbonded pdb=" O PHE A 392 " pdb=" H THR A 523 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN A 474 " pdb=" H GLN A 474 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN H 13 " pdb=" H GLN H 13 " model vdw 1.668 2.450 nonbonded pdb=" OD1 ASP H 109 " pdb=" H VAL H 110 " model vdw 1.671 2.450 ... (remaining 83206 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 0.046 3419 Z= 0.185 Angle : 0.584 4.978 4647 Z= 0.327 Chirality : 0.043 0.133 492 Planarity : 0.005 0.051 605 Dihedral : 13.977 79.788 1231 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.62 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -2.94 (0.38), residues: 420 helix: -3.67 (0.71), residues: 21 sheet: -1.29 (0.47), residues: 122 loop : -2.24 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 41 HIS 0.002 0.001 HIS L 96 PHE 0.014 0.001 PHE L 77 TYR 0.013 0.001 TYR A 380 ARG 0.001 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8760 (m-30) cc_final: 0.8492 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4182 time to fit residues: 40.4917 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.044117 restraints weight = 50251.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046876 restraints weight = 21421.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.048758 restraints weight = 11499.326| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3419 Z= 0.219 Angle : 0.567 4.837 4647 Z= 0.307 Chirality : 0.041 0.134 492 Planarity : 0.005 0.049 605 Dihedral : 5.645 42.684 494 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -2.86 (0.39), residues: 420 helix: -3.01 (0.80), residues: 27 sheet: -1.31 (0.47), residues: 123 loop : -2.17 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE L 77 TYR 0.019 0.001 TYR A 489 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.9455 (ttm110) cc_final: 0.9041 (mtp85) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3990 time to fit residues: 32.8070 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041469 restraints weight = 51923.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.044078 restraints weight = 22050.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045868 restraints weight = 11905.898| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3419 Z= 0.256 Angle : 0.578 5.268 4647 Z= 0.313 Chirality : 0.040 0.126 492 Planarity : 0.006 0.079 605 Dihedral : 5.459 35.679 494 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -2.72 (0.39), residues: 420 helix: -3.20 (0.81), residues: 27 sheet: -1.24 (0.47), residues: 123 loop : -2.02 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.002 HIS L 96 PHE 0.020 0.002 PHE A 486 TYR 0.017 0.002 TYR A 489 ARG 0.018 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLN cc_start: 0.9398 (pm20) cc_final: 0.8826 (tt0) REVERT: A 484 GLU cc_start: 0.7737 (tp30) cc_final: 0.7493 (tp30) REVERT: H 59 TYR cc_start: 0.8730 (m-80) cc_final: 0.8227 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.4216 time to fit residues: 33.1296 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042232 restraints weight = 52591.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.044783 restraints weight = 22359.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046602 restraints weight = 12058.354| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3419 Z= 0.176 Angle : 0.536 5.200 4647 Z= 0.289 Chirality : 0.040 0.139 492 Planarity : 0.006 0.076 605 Dihedral : 5.269 36.686 494 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.47 (0.40), residues: 420 helix: -3.05 (0.83), residues: 27 sheet: -1.08 (0.46), residues: 123 loop : -1.82 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS L 96 PHE 0.014 0.001 PHE L 77 TYR 0.012 0.001 TYR A 489 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9003 (t0) cc_final: 0.8767 (t0) REVERT: A 471 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 484 GLU cc_start: 0.7877 (tp30) cc_final: 0.7510 (tp30) REVERT: H 59 TYR cc_start: 0.8677 (m-80) cc_final: 0.8199 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.4045 time to fit residues: 33.9239 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.047736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.039598 restraints weight = 54634.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041921 restraints weight = 23962.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.043576 restraints weight = 13143.366| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3419 Z= 0.341 Angle : 0.617 4.846 4647 Z= 0.334 Chirality : 0.040 0.126 492 Planarity : 0.006 0.070 605 Dihedral : 5.523 32.890 494 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -2.60 (0.39), residues: 420 helix: -3.40 (0.74), residues: 27 sheet: -1.02 (0.47), residues: 119 loop : -1.96 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 436 HIS 0.004 0.001 HIS L 96 PHE 0.017 0.002 PHE L 77 TYR 0.010 0.002 TYR H 80 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9103 (t0) cc_final: 0.8854 (t0) REVERT: A 471 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 484 GLU cc_start: 0.7826 (tp30) cc_final: 0.7561 (tp30) REVERT: H 59 TYR cc_start: 0.8860 (m-80) cc_final: 0.8243 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4221 time to fit residues: 30.7800 Evaluate side-chains 52 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.047931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039681 restraints weight = 53380.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042053 restraints weight = 23174.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043711 restraints weight = 12745.716| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3419 Z= 0.233 Angle : 0.571 5.228 4647 Z= 0.308 Chirality : 0.040 0.138 492 Planarity : 0.006 0.068 605 Dihedral : 5.388 34.997 494 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -2.54 (0.40), residues: 420 helix: -3.36 (0.78), residues: 27 sheet: -0.89 (0.46), residues: 124 loop : -1.98 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS L 96 PHE 0.020 0.002 PHE L 77 TYR 0.011 0.001 TYR L 55 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9081 (t0) cc_final: 0.8854 (t0) REVERT: A 484 GLU cc_start: 0.7854 (tp30) cc_final: 0.7506 (tp30) REVERT: H 59 TYR cc_start: 0.8811 (m-80) cc_final: 0.8226 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.4053 time to fit residues: 27.8268 Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.047945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039518 restraints weight = 53779.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.041917 restraints weight = 23234.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043652 restraints weight = 12775.698| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3419 Z= 0.226 Angle : 0.559 5.074 4647 Z= 0.301 Chirality : 0.040 0.134 492 Planarity : 0.005 0.067 605 Dihedral : 5.423 36.306 494 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -2.55 (0.40), residues: 420 helix: -3.43 (0.75), residues: 27 sheet: -0.89 (0.45), residues: 124 loop : -1.98 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS L 96 PHE 0.017 0.002 PHE L 77 TYR 0.008 0.001 TYR A 489 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9518 (t0) cc_final: 0.9191 (t0) REVERT: A 484 GLU cc_start: 0.7789 (tp30) cc_final: 0.7416 (tp30) REVERT: H 59 TYR cc_start: 0.8868 (m-80) cc_final: 0.8396 (m-80) REVERT: L 55 TYR cc_start: 0.9548 (p90) cc_final: 0.9186 (p90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.4042 time to fit residues: 28.2191 Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 68.0293 > 50: distance: 30 - 46: 25.051 distance: 46 - 47: 24.914 distance: 46 - 57: 27.835 distance: 47 - 48: 24.701 distance: 47 - 50: 36.095 distance: 47 - 58: 27.877 distance: 48 - 49: 15.092 distance: 48 - 70: 35.607 distance: 50 - 51: 33.082 distance: 50 - 59: 24.100 distance: 50 - 60: 19.812 distance: 51 - 52: 10.618 distance: 51 - 61: 12.931 distance: 51 - 62: 4.577 distance: 52 - 53: 10.820 distance: 52 - 63: 9.144 distance: 52 - 64: 13.162 distance: 53 - 54: 11.238 distance: 53 - 65: 24.370 distance: 54 - 55: 9.646 distance: 54 - 56: 15.598 distance: 55 - 66: 8.300 distance: 55 - 67: 6.427 distance: 56 - 68: 8.169 distance: 56 - 69: 7.063 distance: 70 - 71: 28.231 distance: 70 - 74: 28.074 distance: 71 - 72: 39.839 distance: 71 - 75: 18.376 distance: 71 - 76: 42.099 distance: 72 - 73: 43.758 distance: 72 - 77: 3.712 distance: 77 - 78: 24.961 distance: 77 - 85: 43.507 distance: 78 - 79: 37.513 distance: 78 - 81: 33.251 distance: 78 - 86: 23.963 distance: 79 - 80: 22.725 distance: 79 - 89: 9.135 distance: 81 - 82: 19.514 distance: 81 - 87: 7.733 distance: 81 - 88: 26.961 distance: 82 - 83: 20.041 distance: 82 - 84: 13.244 distance: 89 - 90: 13.725 distance: 89 - 98: 15.489 distance: 90 - 91: 8.073 distance: 90 - 93: 11.720 distance: 90 - 99: 14.394 distance: 91 - 92: 20.124 distance: 91 - 104: 9.942 distance: 92 - 144: 22.149 distance: 93 - 94: 7.298 distance: 93 - 100: 15.701 distance: 93 - 101: 20.109 distance: 94 - 95: 4.393 distance: 94 - 102: 28.253 distance: 94 - 103: 18.686 distance: 95 - 96: 10.448 distance: 95 - 97: 16.284 distance: 104 - 105: 14.150 distance: 104 - 111: 11.969 distance: 105 - 106: 16.137 distance: 105 - 108: 10.630 distance: 105 - 112: 9.772 distance: 106 - 107: 18.140 distance: 106 - 120: 16.402 distance: 107 - 161: 13.303 distance: 108 - 109: 16.245 distance: 108 - 110: 3.245 distance: 108 - 113: 9.807 distance: 109 - 114: 9.711 distance: 109 - 115: 4.208 distance: 109 - 116: 7.100 distance: 110 - 117: 4.867 distance: 110 - 118: 8.318 distance: 110 - 119: 8.216 distance: 120 - 121: 9.157 distance: 120 - 131: 15.623 distance: 121 - 122: 5.008 distance: 121 - 124: 8.466 distance: 121 - 132: 6.433 distance: 122 - 144: 8.589 distance: 124 - 125: 8.796 distance: 124 - 133: 9.758 distance: 124 - 134: 4.238 distance: 125 - 126: 10.083 distance: 125 - 135: 13.170 distance: 125 - 136: 10.319 distance: 126 - 127: 4.141 distance: 126 - 137: 10.550 distance: 126 - 138: 10.018 distance: 127 - 128: 7.702 distance: 127 - 139: 7.579 distance: 128 - 129: 5.926 distance: 128 - 130: 5.112 distance: 129 - 140: 4.824 distance: 129 - 141: 4.879 distance: 130 - 142: 4.515 distance: 130 - 143: 5.359 distance: 144 - 153: 15.916 distance: 145 - 146: 6.805 distance: 145 - 148: 8.386 distance: 145 - 154: 11.353 distance: 146 - 147: 5.825 distance: 146 - 161: 11.279 distance: 148 - 149: 11.301 distance: 148 - 155: 7.958 distance: 148 - 156: 13.806 distance: 149 - 150: 9.777 distance: 149 - 157: 22.933 distance: 149 - 158: 11.208 distance: 150 - 151: 15.636 distance: 150 - 152: 14.296 distance: 152 - 159: 16.320 distance: 152 - 160: 7.777 distance: 161 - 162: 17.691 distance: 161 - 169: 4.861 distance: 162 - 163: 9.535 distance: 162 - 165: 8.905 distance: 162 - 170: 10.302 distance: 163 - 164: 17.091 distance: 163 - 180: 11.347 distance: 165 - 166: 18.095 distance: 165 - 167: 3.627 distance: 165 - 171: 3.676 distance: 166 - 168: 3.501 distance: 166 - 172: 7.900 distance: 167 - 174: 9.722 distance: 167 - 175: 6.751 distance: 167 - 176: 8.845 distance: 168 - 178: 3.238 distance: 180 - 181: 27.563 distance: 180 - 185: 26.211 distance: 181 - 182: 30.807 distance: 181 - 184: 15.831 distance: 181 - 186: 12.268 distance: 182 - 183: 39.748 distance: 182 - 190: 26.564 distance: 184 - 187: 6.204 distance: 184 - 188: 20.616 distance: 184 - 189: 23.469 distance: 190 - 191: 36.970 distance: 190 - 196: 18.297 distance: 191 - 192: 29.774 distance: 191 - 194: 20.042 distance: 191 - 197: 37.101 distance: 192 - 193: 13.743 distance: 192 - 204: 9.504 distance: 194 - 195: 17.930 distance: 194 - 198: 18.115 distance: 194 - 199: 14.005 distance: 195 - 196: 24.149 distance: 195 - 200: 11.272 distance: 195 - 201: 15.220 distance: 196 - 202: 13.018 distance: 196 - 203: 13.655