Starting phenix.real_space_refine on Mon Sep 23 19:11:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/09_2024/8pkd_17735.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/09_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_17735/09_2024/8pkd_17735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/09_2024/8pkd_17735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/09_2024/8pkd_17735.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkd_17735/09_2024/8pkd_17735.cif" } 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. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.57, per 1000 atoms: 0.74 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 552.7 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: 0.53 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: 1.17 Time building geometry restraints manager: 1.34 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: 0.00 - 1.02: 6543 1.02 - 2.05: 159 2.05 - 3.07: 46 3.07 - 4.10: 4 4.10 - 5.12: 4 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 3.120 nonbonded pdb=" O PHE C 102 " pdb=" ND2 ASN C 106 " model vdw 2.339 3.120 nonbonded pdb=" OE1 GLU A 44 " pdb=" NE2 HIS D 32 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASP D 7 " pdb=" NH2 ARG D 10 " model vdw 2.345 3.120 nonbonded pdb=" OD1 ASP C 7 " pdb=" NH2 ARG C 10 " model vdw 2.347 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.060 Find NCS groups from input model: 0.150 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:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- 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 : 0.531 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: 1.6372 time to fit residues: 195.3335 Evaluate side-chains 81 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 0.6980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 124 GLN B 17 GLN B 31 ASN C 31 ASN C 124 GLN D 17 GLN D 124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4960 Z= 0.206 Angle : 0.470 5.360 6756 Z= 0.263 Chirality : 0.041 0.138 704 Planarity : 0.004 0.035 896 Dihedral : 3.893 12.581 656 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.41 % Allowed : 4.92 % 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: 1.75 (0.34), residues: 592 helix: 1.45 (0.28), residues: 348 sheet: 2.63 (0.50), residues: 72 loop : 0.00 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 18 HIS 0.002 0.001 HIS A 132 PHE 0.009 0.001 PHE C 102 TYR 0.008 0.001 TYR C 118 ARG 0.004 0.000 ARG D 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 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.549 Fit side-chains REVERT: A 3 ASN cc_start: 0.6693 (m-40) cc_final: 0.5736 (t0) REVERT: A 75 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: A 123 ARG cc_start: 0.7695 (mmt-90) cc_final: 0.7476 (mmp80) REVERT: A 148 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7220 (mmt90) REVERT: B 3 ASN cc_start: 0.6802 (m-40) cc_final: 0.5783 (t0) REVERT: B 148 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7389 (mmt90) REVERT: C 3 ASN cc_start: 0.6500 (m-40) cc_final: 0.5479 (t0) REVERT: C 148 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7405 (mmt90) REVERT: D 3 ASN cc_start: 0.6662 (m-40) cc_final: 0.5718 (t0) REVERT: D 27 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8135 (tp-100) REVERT: D 148 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7265 (mmt90) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 1.6391 time to fit residues: 150.1564 Evaluate side-chains 79 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4960 Z= 0.156 Angle : 0.428 5.311 6756 Z= 0.238 Chirality : 0.038 0.131 704 Planarity : 0.004 0.035 896 Dihedral : 3.900 11.912 656 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.41 % Allowed : 6.15 % Favored : 93.44 % 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: 1.86 (0.34), residues: 592 helix: 1.61 (0.28), residues: 348 sheet: 2.48 (0.50), residues: 72 loop : -0.00 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 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 0.002 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 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.565 Fit side-chains REVERT: A 3 ASN cc_start: 0.6622 (m-40) cc_final: 0.5674 (t0) REVERT: A 123 ARG cc_start: 0.7708 (mmt-90) cc_final: 0.7482 (mmp80) REVERT: A 148 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7208 (mmt90) REVERT: B 3 ASN cc_start: 0.6687 (m-40) cc_final: 0.5644 (t0) REVERT: B 148 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7385 (mmt90) REVERT: C 3 ASN cc_start: 0.6477 (m-40) cc_final: 0.5412 (t0) REVERT: C 148 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7378 (mmt90) REVERT: D 3 ASN cc_start: 0.6601 (m-40) cc_final: 0.5622 (t0) REVERT: D 75 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: D 148 ARG cc_start: 0.7609 (mtp180) cc_final: 0.7242 (mmt90) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 1.5655 time to fit residues: 143.5488 Evaluate side-chains 79 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS C 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4960 Z= 0.287 Angle : 0.523 5.372 6756 Z= 0.296 Chirality : 0.043 0.151 704 Planarity : 0.004 0.038 896 Dihedral : 4.491 21.458 656 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.02 % Allowed : 6.56 % Favored : 92.42 % 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: 1.53 (0.29), residues: 344 sheet: 2.34 (0.49), residues: 72 loop : 0.34 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 18 HIS 0.003 0.001 HIS B 93 PHE 0.007 0.002 PHE D 88 TYR 0.009 0.002 TYR B 118 ARG 0.003 0.001 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 90 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.512 Fit side-chains REVERT: A 3 ASN cc_start: 0.6643 (m-40) cc_final: 0.5627 (t0) REVERT: A 75 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: A 148 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7236 (mmt90) REVERT: B 3 ASN cc_start: 0.6635 (m-40) cc_final: 0.5558 (t0) REVERT: B 148 ARG cc_start: 0.7717 (mtp180) cc_final: 0.7417 (mmt90) REVERT: C 3 ASN cc_start: 0.6447 (m-40) cc_final: 0.5354 (t0) REVERT: C 148 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7386 (mmt90) REVERT: D 3 ASN cc_start: 0.6622 (m-40) cc_final: 0.5563 (t0) REVERT: D 44 GLU cc_start: 0.8265 (tt0) cc_final: 0.7983 (tt0) REVERT: D 75 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: D 148 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7269 (mmt90) outliers start: 5 outliers final: 2 residues processed: 90 average time/residue: 1.6297 time to fit residues: 150.9282 Evaluate side-chains 82 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 77 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 B 37 GLN C 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2689 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= 0.134 Angle : 0.417 5.245 6756 Z= 0.232 Chirality : 0.038 0.130 704 Planarity : 0.004 0.036 896 Dihedral : 4.079 17.102 656 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.82 % Allowed : 6.56 % Favored : 92.62 % 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: 1.92 (0.34), residues: 592 helix: 1.65 (0.28), residues: 348 sheet: 2.30 (0.48), residues: 72 loop : 0.15 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 18 HIS 0.001 0.000 HIS B 93 PHE 0.006 0.001 PHE B 88 TYR 0.009 0.001 TYR B 118 ARG 0.002 0.000 ARG A 123 *********************** 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 91 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.525 Fit side-chains REVERT: A 3 ASN cc_start: 0.6599 (m-40) cc_final: 0.5599 (t0) REVERT: A 44 GLU cc_start: 0.8340 (tt0) cc_final: 0.8040 (tt0) REVERT: A 75 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8477 (mt0) REVERT: A 148 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7198 (mmt90) REVERT: B 3 ASN cc_start: 0.6607 (m-40) cc_final: 0.5549 (t0) REVERT: B 148 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7389 (mmt90) REVERT: C 3 ASN cc_start: 0.6426 (m-40) cc_final: 0.5320 (t0) REVERT: C 148 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7384 (mmt90) REVERT: D 3 ASN cc_start: 0.6595 (m-40) cc_final: 0.5560 (t0) REVERT: D 75 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: D 148 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7213 (mmt90) outliers start: 4 outliers final: 2 residues processed: 91 average time/residue: 1.5498 time to fit residues: 145.4177 Evaluate side-chains 84 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS C 32 HIS D 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4960 Z= 0.127 Angle : 0.405 5.246 6756 Z= 0.225 Chirality : 0.038 0.127 704 Planarity : 0.003 0.037 896 Dihedral : 3.933 14.695 656 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.82 % Allowed : 7.58 % Favored : 91.60 % 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: 2.00 (0.34), residues: 592 helix: 1.74 (0.28), residues: 348 sheet: 2.22 (0.49), residues: 72 loop : 0.16 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 18 HIS 0.001 0.000 HIS C 32 PHE 0.006 0.001 PHE B 88 TYR 0.008 0.001 TYR B 118 ARG 0.002 0.000 ARG B 123 *********************** 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 90 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.539 Fit side-chains REVERT: A 3 ASN cc_start: 0.6609 (m-40) cc_final: 0.5604 (t0) REVERT: A 75 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: A 148 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7216 (mmt90) REVERT: B 3 ASN cc_start: 0.6590 (m-40) cc_final: 0.5537 (t0) REVERT: B 148 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7338 (mmt90) REVERT: C 3 ASN cc_start: 0.6382 (m-40) cc_final: 0.5308 (t0) REVERT: C 148 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7333 (mmt90) REVERT: D 3 ASN cc_start: 0.6573 (m-40) cc_final: 0.5514 (t0) REVERT: D 75 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: D 148 ARG cc_start: 0.7584 (mtp180) cc_final: 0.7226 (mmt90) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 1.5910 time to fit residues: 147.4630 Evaluate side-chains 85 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS C 32 HIS D 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2788 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= 0.142 Angle : 0.418 5.248 6756 Z= 0.233 Chirality : 0.038 0.128 704 Planarity : 0.003 0.037 896 Dihedral : 4.000 16.037 656 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.82 % Allowed : 7.99 % Favored : 91.19 % 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: 2.00 (0.35), residues: 592 helix: 1.73 (0.28), residues: 348 sheet: 2.27 (0.50), residues: 72 loop : 0.16 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 18 HIS 0.001 0.000 HIS B 32 PHE 0.006 0.001 PHE B 88 TYR 0.009 0.001 TYR C 118 ARG 0.002 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.551 Fit side-chains REVERT: A 3 ASN cc_start: 0.6615 (m-40) cc_final: 0.5602 (t0) REVERT: A 75 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: A 148 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7206 (mmt90) REVERT: B 3 ASN cc_start: 0.6574 (m-40) cc_final: 0.5488 (t0) REVERT: B 148 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7337 (mmt90) REVERT: C 3 ASN cc_start: 0.6394 (m-40) cc_final: 0.5311 (t0) REVERT: C 148 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7334 (mmt90) REVERT: D 3 ASN cc_start: 0.6565 (m-40) cc_final: 0.5517 (t0) REVERT: D 75 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: D 148 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7231 (mmt90) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 1.6092 time to fit residues: 147.5034 Evaluate side-chains 84 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 D 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2800 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= 0.143 Angle : 0.418 5.241 6756 Z= 0.233 Chirality : 0.038 0.129 704 Planarity : 0.003 0.037 896 Dihedral : 4.022 17.102 656 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.82 % Allowed : 7.99 % Favored : 91.19 % 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: 2.01 (0.35), residues: 592 helix: 1.74 (0.28), residues: 348 sheet: 2.28 (0.50), residues: 72 loop : 0.17 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 18 HIS 0.001 0.001 HIS C 32 PHE 0.006 0.001 PHE D 88 TYR 0.009 0.001 TYR C 118 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.623 Fit side-chains REVERT: A 3 ASN cc_start: 0.6611 (m-40) cc_final: 0.5599 (t0) REVERT: A 75 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: A 148 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7184 (mmt90) REVERT: B 3 ASN cc_start: 0.6571 (m-40) cc_final: 0.6107 (t0) REVERT: B 148 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7360 (mmt90) REVERT: C 3 ASN cc_start: 0.6380 (m-40) cc_final: 0.5277 (t0) REVERT: C 148 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7332 (mmt90) REVERT: D 3 ASN cc_start: 0.6564 (m-40) cc_final: 0.5541 (t0) REVERT: D 75 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: D 148 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7228 (mmt90) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 1.6310 time to fit residues: 149.6289 Evaluate side-chains 85 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 D 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4960 Z= 0.119 Angle : 0.399 5.231 6756 Z= 0.221 Chirality : 0.037 0.123 704 Planarity : 0.003 0.037 896 Dihedral : 3.884 15.199 656 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.02 % Allowed : 7.79 % Favored : 91.19 % 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: 2.08 (0.34), residues: 592 helix: 1.80 (0.28), residues: 348 sheet: 2.31 (0.51), residues: 72 loop : 0.16 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 18 HIS 0.002 0.000 HIS C 32 PHE 0.006 0.001 PHE D 88 TYR 0.008 0.001 TYR C 118 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 9 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: 5 poor density : 83 time to evaluate : 0.554 Fit side-chains REVERT: A 3 ASN cc_start: 0.6607 (m-40) cc_final: 0.5597 (t0) REVERT: A 75 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: A 148 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7183 (mmt90) REVERT: B 3 ASN cc_start: 0.6591 (m-40) cc_final: 0.6105 (t0) REVERT: B 44 GLU cc_start: 0.8339 (tt0) cc_final: 0.8083 (tt0) REVERT: B 148 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7365 (mmt90) REVERT: C 3 ASN cc_start: 0.6381 (m-40) cc_final: 0.5318 (t0) REVERT: C 148 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7330 (mmt90) REVERT: D 3 ASN cc_start: 0.6559 (m-40) cc_final: 0.5520 (t0) REVERT: D 75 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: D 148 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7229 (mmt90) outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 1.6388 time to fit residues: 148.7624 Evaluate side-chains 83 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS C 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4960 Z= 0.201 Angle : 0.460 5.309 6756 Z= 0.259 Chirality : 0.040 0.137 704 Planarity : 0.004 0.038 896 Dihedral : 4.258 20.504 656 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.02 % Allowed : 7.99 % Favored : 90.98 % 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: 2.09 (0.35), residues: 592 helix: 1.74 (0.29), residues: 344 sheet: 2.33 (0.50), residues: 72 loop : 0.36 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 18 HIS 0.002 0.001 HIS C 93 PHE 0.007 0.001 PHE D 88 TYR 0.009 0.001 TYR D 118 ARG 0.002 0.000 ARG D 19 ********************** REFINEMENT MACRO_CYCLE 10 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: 5 poor density : 83 time to evaluate : 0.479 Fit side-chains REVERT: A 3 ASN cc_start: 0.6636 (m-40) cc_final: 0.5612 (t0) REVERT: A 75 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: A 148 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7185 (mmt90) REVERT: B 3 ASN cc_start: 0.6578 (m-40) cc_final: 0.6092 (t0) REVERT: B 148 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7362 (mmt90) REVERT: C 3 ASN cc_start: 0.6426 (m-40) cc_final: 0.5284 (t0) REVERT: C 148 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7378 (mmt90) REVERT: D 3 ASN cc_start: 0.6578 (m-40) cc_final: 0.5515 (t0) REVERT: D 75 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: D 148 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7227 (mmt90) outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 1.6815 time to fit residues: 152.3288 Evaluate side-chains 83 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 D 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111621 restraints weight = 4330.785| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.65 r_work: 0.2921 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4960 Z= 0.122 Angle : 0.402 5.218 6756 Z= 0.223 Chirality : 0.037 0.123 704 Planarity : 0.003 0.037 896 Dihedral : 3.957 16.877 656 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.82 % Allowed : 8.20 % Favored : 90.98 % 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: 2.07 (0.35), residues: 592 helix: 1.78 (0.28), residues: 348 sheet: 2.35 (0.51), residues: 72 loop : 0.18 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 18 HIS 0.002 0.000 HIS C 32 PHE 0.006 0.001 PHE B 88 TYR 0.009 0.001 TYR C 118 ARG 0.002 0.000 ARG B 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.96 seconds wall clock time: 49 minutes 21.72 seconds (2961.72 seconds total)