Starting phenix.real_space_refine on Mon Jun 24 20:27:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/06_2024/8pkd_17735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/06_2024/8pkd_17735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/06_2024/8pkd_17735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/06_2024/8pkd_17735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/06_2024/8pkd_17735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/06_2024/8pkd_17735.pdb" } resolution = 2.33 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= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 3048 2.51 5 N 872 2.21 5 O 916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4844 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1207 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "B" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1207 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "C" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1207 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "D" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1207 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.62, per 1000 atoms: 0.75 Number of scatterers: 4844 At special positions: 0 Unit cell: (72.927, 79.497, 77.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 916 8.00 N 872 7.00 C 3048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 871.6 milliseconds 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 59.5% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 34 through 53 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.848A pdb=" N THR A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.592A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.764A pdb=" N GLU A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.859A pdb=" N THR B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.605A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.766A pdb=" N GLU B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 34 through 53 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.845A pdb=" N THR C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.556A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.750A pdb=" N GLU C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.827A pdb=" N THR D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.574A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.743A pdb=" N GLU D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 3.725A pdb=" N LEU A 89 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 85 removed outlier: 3.638A pdb=" N LEU B 89 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 79 through 85 removed outlier: 3.697A pdb=" N LEU C 89 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 85 removed outlier: 3.673A pdb=" N LEU D 89 " --> pdb=" O LEU D 149 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 843 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: 1.26 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1656 1.34 - 1.46: 1076 1.46 - 1.57: 2212 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 4960 Sorted by residual: bond pdb=" C ALA D 96 " pdb=" N PRO D 97 " ideal model delta sigma weight residual 1.334 1.328 0.006 8.40e-03 1.42e+04 4.32e-01 bond pdb=" CA ALA D 101 " pdb=" CB ALA D 101 " ideal model delta sigma weight residual 1.533 1.525 0.008 1.46e-02 4.69e+03 2.77e-01 bond pdb=" CB TRP C 18 " pdb=" CG TRP C 18 " ideal model delta sigma weight residual 1.498 1.482 0.016 3.10e-02 1.04e+03 2.74e-01 bond pdb=" CB TRP A 18 " pdb=" CG TRP A 18 " ideal model delta sigma weight residual 1.498 1.483 0.015 3.10e-02 1.04e+03 2.41e-01 bond pdb=" CB TRP D 18 " pdb=" CG TRP D 18 " ideal model delta sigma weight residual 1.498 1.483 0.015 3.10e-02 1.04e+03 2.39e-01 ... (remaining 4955 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.28: 181 107.28 - 113.98: 2675 113.98 - 120.69: 2166 120.69 - 127.40: 1645 127.40 - 134.10: 89 Bond angle restraints: 6756 Sorted by residual: angle pdb=" CA ASN B 3 " pdb=" C ASN B 3 " pdb=" N PRO B 4 " ideal model delta sigma weight residual 118.44 121.26 -2.82 1.59e+00 3.96e-01 3.15e+00 angle pdb=" N GLU D 59 " pdb=" CA GLU D 59 " pdb=" C GLU D 59 " ideal model delta sigma weight residual 113.18 111.07 2.11 1.33e+00 5.65e-01 2.53e+00 angle pdb=" N GLU C 59 " pdb=" CA GLU C 59 " pdb=" C GLU C 59 " ideal model delta sigma weight residual 113.18 111.19 1.99 1.33e+00 5.65e-01 2.23e+00 angle pdb=" N GLU A 59 " pdb=" CA GLU A 59 " pdb=" C GLU A 59 " ideal model delta sigma weight residual 113.18 111.40 1.78 1.33e+00 5.65e-01 1.78e+00 angle pdb=" N ASN B 3 " pdb=" CA ASN B 3 " pdb=" C ASN B 3 " ideal model delta sigma weight residual 109.81 112.67 -2.86 2.21e+00 2.05e-01 1.68e+00 ... (remaining 6751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2578 17.71 - 35.42: 229 35.42 - 53.14: 39 53.14 - 70.85: 13 70.85 - 88.56: 9 Dihedral angle restraints: 2868 sinusoidal: 1128 harmonic: 1740 Sorted by residual: dihedral pdb=" CG ARG D 19 " pdb=" CD ARG D 19 " pdb=" NE ARG D 19 " pdb=" CZ ARG D 19 " ideal model delta sinusoidal sigma weight residual 90.00 134.28 -44.28 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG C 43 " pdb=" CD ARG C 43 " pdb=" NE ARG C 43 " pdb=" CZ ARG C 43 " ideal model delta sinusoidal sigma weight residual -90.00 -128.71 38.71 2 1.50e+01 4.44e-03 8.34e+00 dihedral pdb=" CG ARG B 43 " pdb=" CD ARG B 43 " pdb=" NE ARG B 43 " pdb=" CZ ARG B 43 " ideal model delta sinusoidal sigma weight residual -90.00 -128.40 38.40 2 1.50e+01 4.44e-03 8.23e+00 ... (remaining 2865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 383 0.024 - 0.049: 188 0.049 - 0.073: 86 0.073 - 0.097: 27 0.097 - 0.122: 20 Chirality restraints: 704 Sorted by residual: chirality pdb=" CA PRO D 35 " pdb=" N PRO D 35 " pdb=" C PRO D 35 " pdb=" CB PRO D 35 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA PRO C 35 " pdb=" N PRO C 35 " pdb=" C PRO C 35 " pdb=" CB PRO C 35 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PRO B 35 " pdb=" N PRO B 35 " pdb=" C PRO B 35 " pdb=" CB PRO B 35 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 701 not shown) Planarity restraints: 896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 34 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO D 35 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 35 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 35 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 34 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 35 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 35 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 35 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 34 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 35 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.019 5.00e-02 4.00e+02 ... (remaining 893 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1000 2.78 - 3.31: 4544 3.31 - 3.84: 8294 3.84 - 4.37: 9896 4.37 - 4.90: 16647 Nonbonded interactions: 40381 Sorted by model distance: nonbonded pdb=" NE2 HIS A 32 " pdb=" OE1 GLU D 44 " model vdw 2.246 2.520 nonbonded pdb=" O PHE C 102 " pdb=" ND2 ASN C 106 " model vdw 2.339 2.520 nonbonded pdb=" OE1 GLU A 44 " pdb=" NE2 HIS D 32 " model vdw 2.342 2.520 nonbonded pdb=" OD1 ASP D 7 " pdb=" NH2 ARG D 10 " model vdw 2.345 2.520 nonbonded pdb=" OD1 ASP C 7 " pdb=" NH2 ARG C 10 " model vdw 2.347 2.520 ... (remaining 40376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.810 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.090 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.020 4960 Z= 0.193 Angle : 0.441 5.120 6756 Z= 0.243 Chirality : 0.038 0.122 704 Planarity : 0.003 0.034 896 Dihedral : 15.001 88.562 1740 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.55 (0.34), residues: 592 helix: 1.22 (0.28), residues: 352 sheet: 2.88 (0.48), residues: 72 loop : -0.10 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 109 HIS 0.002 0.001 HIS C 32 PHE 0.006 0.001 PHE C 113 TYR 0.008 0.001 TYR D 94 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.554 Fit side-chains REVERT: A 3 ASN cc_start: 0.6793 (m-40) cc_final: 0.5790 (t0) REVERT: A 148 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7168 (mmt90) REVERT: B 3 ASN cc_start: 0.6899 (m-40) cc_final: 0.5964 (t0) REVERT: B 47 GLN cc_start: 0.7599 (mt0) cc_final: 0.7364 (mt0) REVERT: B 148 ARG cc_start: 0.7348 (mtp180) cc_final: 0.7130 (mmt90) REVERT: C 3 ASN cc_start: 0.6720 (m-40) cc_final: 0.5710 (t0) REVERT: C 44 GLU cc_start: 0.8389 (tt0) cc_final: 0.8182 (tt0) REVERT: C 47 GLN cc_start: 0.7751 (mt0) cc_final: 0.7420 (mt0) REVERT: C 52 GLN cc_start: 0.8089 (mm110) cc_final: 0.7779 (mp10) REVERT: C 148 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7217 (mmt90) REVERT: D 3 ASN cc_start: 0.6761 (m-40) cc_final: 0.5797 (t0) REVERT: D 27 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7820 (tp-100) REVERT: D 148 ARG cc_start: 0.7461 (mtp180) cc_final: 0.7167 (mmt90) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.5583 time to fit residues: 186.0825 Evaluate side-chains 81 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 17 GLN C 31 ASN C 124 GLN D 17 GLN D 124 GLN D 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4960 Z= 0.249 Angle : 0.506 5.336 6756 Z= 0.284 Chirality : 0.042 0.144 704 Planarity : 0.004 0.037 896 Dihedral : 4.064 12.970 656 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: 1.81 (0.34), residues: 592 helix: 1.46 (0.28), residues: 344 sheet: 2.62 (0.49), residues: 72 loop : 0.19 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 18 HIS 0.002 0.001 HIS B 93 PHE 0.010 0.002 PHE C 102 TYR 0.010 0.001 TYR B 118 ARG 0.003 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.549 Fit side-chains REVERT: A 3 ASN cc_start: 0.6661 (m-40) cc_final: 0.5706 (t0) REVERT: A 148 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7209 (mmt90) REVERT: B 3 ASN cc_start: 0.6753 (m-40) cc_final: 0.5726 (t0) REVERT: B 148 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7399 (mmt90) REVERT: C 3 ASN cc_start: 0.6514 (m-40) cc_final: 0.5474 (t0) REVERT: C 148 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7401 (mmt90) REVERT: D 3 ASN cc_start: 0.6646 (m-40) cc_final: 0.5701 (t0) REVERT: D 148 ARG cc_start: 0.7623 (mtp180) cc_final: 0.7252 (mmt90) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.7816 time to fit residues: 156.0240 Evaluate side-chains 78 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4960 Z= 0.141 Angle : 0.416 5.305 6756 Z= 0.231 Chirality : 0.038 0.130 704 Planarity : 0.003 0.036 896 Dihedral : 3.852 12.739 656 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.82 % Allowed : 5.12 % Favored : 94.06 % 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: 1.88 (0.34), residues: 592 helix: 1.59 (0.28), residues: 348 sheet: 2.62 (0.49), residues: 72 loop : -0.00 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 18 HIS 0.002 0.001 HIS A 32 PHE 0.006 0.001 PHE D 88 TYR 0.009 0.001 TYR B 118 ARG 0.001 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.555 Fit side-chains REVERT: A 3 ASN cc_start: 0.6652 (m-40) cc_final: 0.5664 (t0) REVERT: A 32 HIS cc_start: 0.8397 (m170) cc_final: 0.8152 (m-70) REVERT: A 44 GLU cc_start: 0.8265 (tt0) cc_final: 0.7914 (tt0) REVERT: A 75 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: A 148 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7206 (mmt90) REVERT: B 3 ASN cc_start: 0.6687 (m-40) cc_final: 0.5646 (t0) REVERT: B 32 HIS cc_start: 0.8419 (m170) cc_final: 0.8175 (m-70) REVERT: B 148 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7392 (mmt90) REVERT: C 3 ASN cc_start: 0.6496 (m-40) cc_final: 0.5423 (t0) REVERT: C 148 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7375 (mmt90) REVERT: D 3 ASN cc_start: 0.6612 (m-40) cc_final: 0.5626 (t0) REVERT: D 75 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: D 148 ARG cc_start: 0.7613 (mtp180) cc_final: 0.7247 (mmt90) outliers start: 4 outliers final: 0 residues processed: 92 average time/residue: 1.5843 time to fit residues: 150.1872 Evaluate side-chains 84 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain D residue 75 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4960 Z= 0.188 Angle : 0.453 5.319 6756 Z= 0.254 Chirality : 0.040 0.139 704 Planarity : 0.004 0.037 896 Dihedral : 4.149 18.236 656 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.61 % Allowed : 5.74 % Favored : 93.65 % 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: 1.96 (0.34), residues: 592 helix: 1.64 (0.29), residues: 344 sheet: 2.49 (0.49), residues: 72 loop : 0.21 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 18 HIS 0.002 0.001 HIS B 93 PHE 0.006 0.001 PHE D 88 TYR 0.008 0.001 TYR C 118 ARG 0.002 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.586 Fit side-chains REVERT: A 3 ASN cc_start: 0.6639 (m-40) cc_final: 0.5631 (t0) REVERT: A 44 GLU cc_start: 0.8289 (tt0) cc_final: 0.7883 (tt0) REVERT: A 75 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: A 148 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7186 (mmt90) REVERT: B 3 ASN cc_start: 0.6632 (m-40) cc_final: 0.5553 (t0) REVERT: B 44 GLU cc_start: 0.8314 (tt0) cc_final: 0.8018 (tt0) REVERT: B 148 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7376 (mmt90) REVERT: C 3 ASN cc_start: 0.6451 (m-40) cc_final: 0.5351 (t0) REVERT: C 148 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7400 (mmt90) REVERT: D 3 ASN cc_start: 0.6636 (m-40) cc_final: 0.5600 (t0) REVERT: D 32 HIS cc_start: 0.8374 (m170) cc_final: 0.8073 (m-70) REVERT: D 75 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: D 148 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7244 (mmt90) outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 1.6474 time to fit residues: 149.2323 Evaluate side-chains 80 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 75 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4960 Z= 0.184 Angle : 0.450 5.292 6756 Z= 0.253 Chirality : 0.039 0.138 704 Planarity : 0.004 0.036 896 Dihedral : 4.187 19.360 656 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.82 % Allowed : 6.35 % Favored : 92.83 % 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: 1.97 (0.34), residues: 592 helix: 1.63 (0.29), residues: 344 sheet: 2.53 (0.49), residues: 72 loop : 0.23 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 18 HIS 0.002 0.000 HIS D 93 PHE 0.007 0.001 PHE D 88 TYR 0.008 0.001 TYR C 118 ARG 0.001 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.557 Fit side-chains REVERT: A 3 ASN cc_start: 0.6630 (m-40) cc_final: 0.5614 (t0) REVERT: A 75 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: A 148 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7190 (mmt90) REVERT: B 3 ASN cc_start: 0.6589 (m-40) cc_final: 0.5509 (t0) REVERT: B 148 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7392 (mmt90) REVERT: C 3 ASN cc_start: 0.6446 (m-40) cc_final: 0.5315 (t0) REVERT: C 148 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7403 (mmt90) REVERT: D 3 ASN cc_start: 0.6630 (m-40) cc_final: 0.5548 (t0) REVERT: D 75 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: D 148 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7217 (mmt90) outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 1.6182 time to fit residues: 148.3850 Evaluate side-chains 83 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 75 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS C 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4960 Z= 0.135 Angle : 0.412 5.247 6756 Z= 0.230 Chirality : 0.038 0.129 704 Planarity : 0.003 0.037 896 Dihedral : 3.978 17.400 656 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.82 % Allowed : 6.35 % Favored : 92.83 % 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: 1.95 (0.34), residues: 592 helix: 1.68 (0.29), residues: 348 sheet: 2.54 (0.48), residues: 72 loop : 0.02 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 18 HIS 0.002 0.000 HIS B 32 PHE 0.006 0.001 PHE D 88 TYR 0.008 0.001 TYR C 118 ARG 0.001 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.535 Fit side-chains REVERT: A 3 ASN cc_start: 0.6636 (m-40) cc_final: 0.5623 (t0) REVERT: A 44 GLU cc_start: 0.8307 (tt0) cc_final: 0.7981 (tt0) REVERT: A 75 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: A 148 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7226 (mmt90) REVERT: B 3 ASN cc_start: 0.6575 (m-40) cc_final: 0.6092 (t0) REVERT: B 148 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7348 (mmt90) REVERT: C 3 ASN cc_start: 0.6427 (m-40) cc_final: 0.5311 (t0) REVERT: C 148 ARG cc_start: 0.7726 (mtp180) cc_final: 0.7389 (mmt90) REVERT: D 3 ASN cc_start: 0.6625 (m-40) cc_final: 0.5549 (t0) REVERT: D 75 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: D 148 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7224 (mmt90) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 1.6625 time to fit residues: 152.2412 Evaluate side-chains 84 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5816 > 50: distance: 63 - 82: 5.530 distance: 72 - 90: 5.915 distance: 75 - 77: 4.243 distance: 76 - 94: 7.643 distance: 78 - 81: 3.966 distance: 79 - 82: 3.066 distance: 80 - 99: 9.818 distance: 82 - 83: 3.563 distance: 83 - 84: 6.127 distance: 83 - 86: 4.323 distance: 84 - 85: 9.325 distance: 84 - 90: 5.644 distance: 85 - 107: 17.005 distance: 87 - 88: 6.436 distance: 87 - 89: 11.233 distance: 90 - 91: 3.208 distance: 91 - 92: 4.069 distance: 92 - 94: 3.095 distance: 93 - 112: 9.261 distance: 94 - 95: 4.214 distance: 95 - 96: 3.583 distance: 97 - 121: 8.348 distance: 99 - 100: 8.249 distance: 100 - 101: 11.382 distance: 100 - 103: 14.895 distance: 101 - 102: 15.937 distance: 101 - 107: 29.897 distance: 102 - 127: 12.816 distance: 103 - 104: 4.185 distance: 104 - 105: 9.105 distance: 104 - 106: 9.727 distance: 107 - 108: 37.709 distance: 108 - 109: 12.279 distance: 108 - 111: 18.445 distance: 109 - 110: 5.337 distance: 109 - 112: 5.043 distance: 110 - 135: 10.118 distance: 112 - 113: 4.072 distance: 113 - 116: 7.096 distance: 114 - 115: 3.397 distance: 114 - 121: 4.363 distance: 115 - 142: 5.784 distance: 116 - 117: 7.237 distance: 117 - 118: 6.586 distance: 118 - 119: 9.282 distance: 118 - 120: 11.515 distance: 121 - 122: 4.950 distance: 122 - 125: 3.922 distance: 123 - 127: 3.049 distance: 124 - 150: 7.244 distance: 125 - 126: 3.773 distance: 127 - 128: 3.305 distance: 128 - 131: 3.403 distance: 129 - 130: 3.768 distance: 129 - 135: 3.811 distance: 130 - 160: 4.814 distance: 131 - 132: 3.447 distance: 132 - 133: 4.055 distance: 132 - 134: 7.457 distance: 136 - 137: 3.986 distance: 136 - 139: 4.581 distance: 137 - 138: 4.936 distance: 139 - 141: 4.446