Starting phenix.real_space_refine on Sun Mar 10 14:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/03_2024/7ykw_33897_updated.pdb" } resolution = 3.6 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= 0.003 sd= 0.040 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 1164 2.51 5 N 356 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 11": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "H" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 1.35, per 1000 atoms: 0.71 Number of scatterers: 1908 At special positions: 0 Unit cell: (86.32, 86.32, 37.44, 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 380 8.00 N 356 7.00 C 1164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 7 " distance=2.03 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: 0.85 Conformation dependent library (CDL) restraints added in 359.8 milliseconds 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 636 1.33 - 1.45: 405 1.45 - 1.57: 883 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 1932 Sorted by residual: bond pdb=" C TYC C 37 " pdb=" NXT TYC C 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C TYC E 37 " pdb=" NXT TYC E 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C TYC B 37 " pdb=" NXT TYC B 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C TYC G 37 " pdb=" NXT TYC G 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C TYC F 37 " pdb=" NXT TYC F 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.73e+01 ... (remaining 1927 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.30: 63 106.30 - 112.55: 990 112.55 - 118.81: 460 118.81 - 125.06: 1099 125.06 - 131.31: 12 Bond angle restraints: 2624 Sorted by residual: angle pdb=" N ALA D 5 " pdb=" CA ALA D 5 " pdb=" C ALA D 5 " ideal model delta sigma weight residual 111.36 104.26 7.10 1.09e+00 8.42e-01 4.24e+01 angle pdb=" N ALA F 5 " pdb=" CA ALA F 5 " pdb=" C ALA F 5 " ideal model delta sigma weight residual 111.28 105.14 6.14 1.09e+00 8.42e-01 3.17e+01 angle pdb=" N PHE F 23 " pdb=" CA PHE F 23 " pdb=" C PHE F 23 " ideal model delta sigma weight residual 108.49 100.04 8.45 1.65e+00 3.67e-01 2.62e+01 angle pdb=" N PHE B 23 " pdb=" CA PHE B 23 " pdb=" C PHE B 23 " ideal model delta sigma weight residual 108.49 100.06 8.43 1.65e+00 3.67e-01 2.61e+01 angle pdb=" N PHE D 23 " pdb=" CA PHE D 23 " pdb=" C PHE D 23 " ideal model delta sigma weight residual 108.49 100.07 8.42 1.65e+00 3.67e-01 2.60e+01 ... (remaining 2619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 992 13.40 - 26.80: 76 26.80 - 40.20: 33 40.20 - 53.60: 20 53.60 - 67.00: 3 Dihedral angle restraints: 1124 sinusoidal: 396 harmonic: 728 Sorted by residual: dihedral pdb=" CB CYS D 2 " pdb=" SG CYS D 2 " pdb=" SG CYS D 7 " pdb=" CB CYS D 7 " ideal model delta sinusoidal sigma weight residual -86.00 -153.00 67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -142.11 56.11 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS H 2 " pdb=" SG CYS H 2 " pdb=" SG CYS H 7 " pdb=" CB CYS H 7 " ideal model delta sinusoidal sigma weight residual -86.00 -141.48 55.48 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 1121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 158 0.047 - 0.094: 78 0.094 - 0.141: 40 0.141 - 0.189: 24 0.189 - 0.236: 16 Chirality restraints: 316 Sorted by residual: chirality pdb=" CA PHE F 23 " pdb=" N PHE F 23 " pdb=" C PHE F 23 " pdb=" CB PHE F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE B 23 " pdb=" N PHE B 23 " pdb=" C PHE B 23 " pdb=" CB PHE B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE D 23 " pdb=" N PHE D 23 " pdb=" C PHE D 23 " pdb=" CB PHE D 23 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 313 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 36 " -0.017 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C THR A 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC A 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 36 " -0.017 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C THR C 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC C 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " -0.017 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C THR E 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1273 3.01 - 3.48: 1825 3.48 - 3.96: 3330 3.96 - 4.43: 3624 4.43 - 4.90: 6480 Nonbonded interactions: 16532 Sorted by model distance: nonbonded pdb=" N ASN F 3 " pdb=" N THR F 4 " model vdw 2.538 2.560 nonbonded pdb=" N ASN B 3 " pdb=" N THR B 4 " model vdw 2.547 2.560 nonbonded pdb=" C THR B 4 " pdb=" OG1 THR B 4 " model vdw 2.561 2.616 nonbonded pdb=" N ASN D 3 " pdb=" N THR D 4 " model vdw 2.567 2.560 nonbonded pdb=" N ASN B 3 " pdb=" O CYS D 2 " model vdw 2.568 2.520 ... (remaining 16527 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.000 Extract box with map and model: 1.840 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.670 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.012 0.105 1932 Z= 0.734 Angle : 1.761 9.681 2624 Z= 1.065 Chirality : 0.087 0.236 316 Planarity : 0.004 0.031 344 Dihedral : 13.038 48.814 632 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % 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: -3.01 (0.43), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 18 PHE 0.011 0.002 PHE E 23 ARG 0.002 0.001 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.231 Fit side-chains REVERT: A 23 PHE cc_start: 0.8129 (m-80) cc_final: 0.6485 (p90) REVERT: B 15 PHE cc_start: 0.7833 (m-80) cc_final: 0.6294 (p90) REVERT: D 14 ASN cc_start: 0.7680 (m-40) cc_final: 0.7330 (m-40) REVERT: F 14 ASN cc_start: 0.7757 (m-40) cc_final: 0.7386 (m-40) REVERT: G 22 ASN cc_start: 0.8296 (t0) cc_final: 0.7862 (t0) REVERT: G 35 ASN cc_start: 0.8321 (m-40) cc_final: 0.8078 (m-40) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0644 time to fit residues: 8.0988 Evaluate side-chains 52 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 31 ASN B 14 ASN B 21 ASN B 31 ASN C 21 ASN C 31 ASN C 35 ASN D 21 ASN D 31 ASN E 21 ASN E 31 ASN F 21 ASN F 31 ASN G 21 ASN G 31 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 31 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1932 Z= 0.246 Angle : 0.607 9.501 2624 Z= 0.287 Chirality : 0.041 0.122 316 Planarity : 0.002 0.010 344 Dihedral : 10.048 56.167 280 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.85 % Allowed : 14.90 % Favored : 81.25 % 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: -3.81 (0.38), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.29), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.013 0.002 PHE D 15 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.228 Fit side-chains REVERT: D 6 THR cc_start: 0.6615 (OUTLIER) cc_final: 0.6400 (t) REVERT: G 22 ASN cc_start: 0.7829 (t0) cc_final: 0.7360 (t0) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.0665 time to fit residues: 5.4692 Evaluate side-chains 51 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 40.0000 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN H 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1932 Z= 0.205 Angle : 0.520 6.604 2624 Z= 0.256 Chirality : 0.039 0.116 316 Planarity : 0.002 0.014 344 Dihedral : 9.350 58.957 280 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.85 % Allowed : 17.31 % Favored : 78.85 % 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: -4.10 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 18 PHE 0.006 0.001 PHE B 15 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.235 Fit side-chains REVERT: F 14 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.6285 (m110) REVERT: G 22 ASN cc_start: 0.7643 (t0) cc_final: 0.7373 (t0) REVERT: H 16 LEU cc_start: 0.7542 (tp) cc_final: 0.6877 (pt) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.0810 time to fit residues: 6.2437 Evaluate side-chains 52 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain H residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1932 Z= 0.292 Angle : 0.557 8.020 2624 Z= 0.273 Chirality : 0.041 0.109 316 Planarity : 0.002 0.010 344 Dihedral : 7.887 45.788 280 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.33 % Allowed : 16.83 % Favored : 78.85 % 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: -4.28 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.28), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.011 0.001 PHE B 15 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.230 Fit side-chains REVERT: E 27 LEU cc_start: 0.8495 (tp) cc_final: 0.8214 (tp) REVERT: G 28 SER cc_start: 0.8814 (t) cc_final: 0.8510 (p) REVERT: H 16 LEU cc_start: 0.7708 (tp) cc_final: 0.7055 (pt) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 0.0689 time to fit residues: 4.9740 Evaluate side-chains 49 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1932 Z= 0.184 Angle : 0.525 9.093 2624 Z= 0.245 Chirality : 0.040 0.109 316 Planarity : 0.001 0.011 344 Dihedral : 6.873 37.081 280 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.37 % Allowed : 18.27 % Favored : 78.37 % 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: -4.38 (0.35), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.27), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 18 PHE 0.006 0.001 PHE F 15 ARG 0.000 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.236 Fit side-chains REVERT: A 15 PHE cc_start: 0.4219 (p90) cc_final: 0.3788 (p90) REVERT: E 27 LEU cc_start: 0.8584 (tp) cc_final: 0.8191 (tp) REVERT: F 14 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6438 (t0) REVERT: G 28 SER cc_start: 0.8672 (t) cc_final: 0.8408 (p) REVERT: H 16 LEU cc_start: 0.7696 (tp) cc_final: 0.6977 (pt) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.0608 time to fit residues: 4.9241 Evaluate side-chains 55 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 1932 Z= 0.480 Angle : 0.604 7.526 2624 Z= 0.303 Chirality : 0.041 0.129 316 Planarity : 0.002 0.014 344 Dihedral : 7.349 36.436 280 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.81 % Allowed : 17.79 % Favored : 77.40 % 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: -4.49 (0.34), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.26), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 18 PHE 0.015 0.002 PHE B 15 ARG 0.001 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.224 Fit side-chains REVERT: H 16 LEU cc_start: 0.7955 (tp) cc_final: 0.7228 (pt) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.0615 time to fit residues: 4.4730 Evaluate side-chains 51 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1932 Z= 0.294 Angle : 0.566 7.503 2624 Z= 0.273 Chirality : 0.040 0.113 316 Planarity : 0.002 0.011 344 Dihedral : 6.818 35.397 280 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.29 % Allowed : 21.15 % Favored : 73.56 % 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: -4.57 (0.34), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.26), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.009 0.001 PHE B 15 ARG 0.001 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.166 Fit side-chains REVERT: D 16 LEU cc_start: 0.8236 (tp) cc_final: 0.7992 (tp) REVERT: H 16 LEU cc_start: 0.7861 (tp) cc_final: 0.7206 (pt) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.0441 time to fit residues: 3.1082 Evaluate side-chains 49 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1932 Z= 0.259 Angle : 0.543 7.042 2624 Z= 0.256 Chirality : 0.040 0.116 316 Planarity : 0.002 0.010 344 Dihedral : 6.512 32.782 280 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.81 % Allowed : 21.15 % Favored : 74.04 % 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: -4.61 (0.34), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.26), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.008 0.001 PHE B 15 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.249 Fit side-chains REVERT: D 16 LEU cc_start: 0.8423 (tp) cc_final: 0.8137 (tp) REVERT: H 16 LEU cc_start: 0.7748 (tp) cc_final: 0.7120 (pt) outliers start: 10 outliers final: 10 residues processed: 47 average time/residue: 0.0585 time to fit residues: 3.7932 Evaluate side-chains 47 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1932 Z= 0.318 Angle : 0.567 7.092 2624 Z= 0.269 Chirality : 0.040 0.120 316 Planarity : 0.002 0.011 344 Dihedral : 6.826 34.012 280 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.29 % Allowed : 22.12 % Favored : 72.60 % 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: -4.62 (0.35), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.010 0.001 PHE B 15 ARG 0.001 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.236 Fit side-chains REVERT: D 16 LEU cc_start: 0.8449 (tp) cc_final: 0.8214 (tp) REVERT: H 16 LEU cc_start: 0.7766 (tp) cc_final: 0.7142 (pt) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.0588 time to fit residues: 3.8962 Evaluate side-chains 47 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 1932 Z= 0.571 Angle : 0.672 7.099 2624 Z= 0.336 Chirality : 0.043 0.141 316 Planarity : 0.002 0.014 344 Dihedral : 8.100 43.972 280 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.33 % Allowed : 24.52 % Favored : 71.15 % 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: -4.76 (0.34), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.26), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 18 PHE 0.017 0.002 PHE B 15 ARG 0.002 0.000 ARG H 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.322 Fit side-chains REVERT: C 15 PHE cc_start: 0.8259 (t80) cc_final: 0.7909 (t80) REVERT: H 16 LEU cc_start: 0.7881 (tp) cc_final: 0.7142 (pt) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.0513 time to fit residues: 3.4260 Evaluate side-chains 43 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.108234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.084879 restraints weight = 5375.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.086781 restraints weight = 2369.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.087892 restraints weight = 1494.179| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 1932 Z= 0.456 Angle : 0.624 7.463 2624 Z= 0.301 Chirality : 0.041 0.130 316 Planarity : 0.002 0.013 344 Dihedral : 7.787 39.149 280 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.33 % Allowed : 23.56 % Favored : 72.12 % 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: -4.79 (0.34), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.26), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.010 0.002 PHE B 15 ARG 0.001 0.000 ARG H 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 889.86 seconds wall clock time: 18 minutes 0.99 seconds (1080.99 seconds total)