Starting phenix.real_space_refine on Sun Mar 10 15:30:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/03_2024/7yl0_33901_updated.pdb" } resolution = 3.2 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= 0.003 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 12 5.16 5 C 1800 2.51 5 N 552 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 2958 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} 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: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} 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: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} 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: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 1.89, per 1000 atoms: 0.64 Number of scatterers: 2958 At special positions: 0 Unit cell: (142.48, 85.28, 42.64, 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 12 16.00 O 594 8.00 N 552 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 7 " distance=2.08 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.02 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.06 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 7 " distance=2.06 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 513.4 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 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: 0.38 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: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 597 1.32 - 1.46: 1114 1.46 - 1.59: 1271 1.59 - 1.73: 0 1.73 - 1.87: 12 Bond restraints: 2994 Sorted by residual: bond pdb=" C THR K 36 " pdb=" N TYC K 37 " ideal model delta sigma weight residual 1.329 1.200 0.129 1.40e-02 5.10e+03 8.46e+01 bond pdb=" C THR H 36 " pdb=" N TYC H 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.40e+01 bond pdb=" C THR G 36 " pdb=" N TYC G 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.39e+01 bond pdb=" C THR J 36 " pdb=" N TYC J 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.37e+01 bond pdb=" C THR L 36 " pdb=" N TYC L 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.35e+01 ... (remaining 2989 not shown) Histogram of bond angle deviations from ideal: 98.10 - 108.45: 299 108.45 - 118.80: 2059 118.80 - 129.15: 1686 129.15 - 139.50: 18 139.50 - 149.85: 6 Bond angle restraints: 4068 Sorted by residual: angle pdb=" C THR F 36 " pdb=" N TYC F 37 " pdb=" CA TYC F 37 " ideal model delta sigma weight residual 121.70 149.85 -28.15 1.80e+00 3.09e-01 2.44e+02 angle pdb=" C THR D 36 " pdb=" N TYC D 37 " pdb=" CA TYC D 37 " ideal model delta sigma weight residual 121.70 149.81 -28.11 1.80e+00 3.09e-01 2.44e+02 angle pdb=" C THR C 36 " pdb=" N TYC C 37 " pdb=" CA TYC C 37 " ideal model delta sigma weight residual 121.70 149.77 -28.07 1.80e+00 3.09e-01 2.43e+02 angle pdb=" C THR E 36 " pdb=" N TYC E 37 " pdb=" CA TYC E 37 " ideal model delta sigma weight residual 121.70 149.74 -28.04 1.80e+00 3.09e-01 2.43e+02 angle pdb=" C THR A 36 " pdb=" N TYC A 37 " pdb=" CA TYC A 37 " ideal model delta sigma weight residual 121.70 149.73 -28.03 1.80e+00 3.09e-01 2.43e+02 ... (remaining 4063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 1614 17.09 - 34.18: 53 34.18 - 51.27: 55 51.27 - 68.35: 19 68.35 - 85.44: 5 Dihedral angle restraints: 1746 sinusoidal: 618 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS A 2 " pdb=" SG CYS A 2 " pdb=" SG CYS A 7 " pdb=" CB CYS A 7 " ideal model delta sinusoidal sigma weight residual 93.00 7.56 85.44 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS E 2 " pdb=" SG CYS E 2 " pdb=" SG CYS E 7 " pdb=" CB CYS E 7 " ideal model delta sinusoidal sigma weight residual 93.00 8.56 84.44 1 1.00e+01 1.00e-02 8.67e+01 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 93.00 9.95 83.05 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 1743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 275 0.065 - 0.130: 142 0.130 - 0.195: 39 0.195 - 0.261: 6 0.261 - 0.326: 30 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL L 32 " pdb=" N VAL L 32 " pdb=" C VAL L 32 " pdb=" CB VAL L 32 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA VAL K 32 " pdb=" N VAL K 32 " pdb=" C VAL K 32 " pdb=" CB VAL K 32 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 489 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " 0.017 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C THR E 36 " -0.049 2.00e-02 2.50e+03 pdb=" O THR E 36 " 0.014 2.00e-02 2.50e+03 pdb=" N TYC E 37 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 36 " 0.017 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C THR F 36 " -0.049 2.00e-02 2.50e+03 pdb=" O THR F 36 " 0.014 2.00e-02 2.50e+03 pdb=" N TYC F 37 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 36 " -0.017 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C THR B 36 " 0.049 2.00e-02 2.50e+03 pdb=" O THR B 36 " -0.014 2.00e-02 2.50e+03 pdb=" N TYC B 37 " -0.018 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1810 2.99 - 3.47: 2612 3.47 - 3.95: 4594 3.95 - 4.42: 5145 4.42 - 4.90: 9391 Nonbonded interactions: 23552 Sorted by model distance: nonbonded pdb=" O THR K 36 " pdb=" CA TYC K 37 " model vdw 2.515 2.776 nonbonded pdb=" O THR J 36 " pdb=" CA TYC J 37 " model vdw 2.515 2.776 nonbonded pdb=" O THR I 36 " pdb=" CA TYC I 37 " model vdw 2.516 2.776 nonbonded pdb=" O THR L 36 " pdb=" CA TYC L 37 " model vdw 2.516 2.776 nonbonded pdb=" O THR H 36 " pdb=" CA TYC H 37 " model vdw 2.516 2.776 ... (remaining 23547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 3.720 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.210 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.016 0.129 2994 Z= 1.056 Angle : 2.509 28.146 4068 Z= 1.518 Chirality : 0.106 0.326 492 Planarity : 0.005 0.029 534 Dihedral : 15.558 60.742 984 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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: -4.14 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 18 PHE 0.027 0.005 PHE K 15 ARG 0.001 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 1 LYS cc_start: 0.5669 (mttt) cc_final: 0.5385 (tttt) REVERT: D 1 LYS cc_start: 0.5886 (mttt) cc_final: 0.5414 (tttt) REVERT: D 7 CYS cc_start: 0.6137 (t) cc_final: 0.5759 (p) REVERT: D 27 LEU cc_start: 0.7326 (tt) cc_final: 0.6989 (mp) REVERT: F 7 CYS cc_start: 0.3823 (t) cc_final: 0.3178 (t) REVERT: K 10 GLN cc_start: 0.6854 (tt0) cc_final: 0.6434 (pm20) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1729 time to fit residues: 25.4635 Evaluate side-chains 70 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 22 ASN H 31 ASN J 14 ASN J 18 HIS J 22 ASN J 31 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN L 22 ASN L 31 ASN A 21 ASN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 HIS G 22 ASN G 31 ASN I 14 ASN I 22 ASN I 31 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN K 18 HIS K 22 ASN K 31 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2994 Z= 0.184 Angle : 0.639 7.158 4068 Z= 0.320 Chirality : 0.044 0.128 492 Planarity : 0.002 0.012 534 Dihedral : 10.303 59.535 432 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.78 % Allowed : 15.43 % Favored : 81.79 % 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: -4.75 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.013 0.002 PHE B 23 ARG 0.001 0.000 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.334 Fit side-chains REVERT: L 34 SER cc_start: 0.8217 (t) cc_final: 0.7927 (p) REVERT: B 27 LEU cc_start: 0.7509 (tt) cc_final: 0.7188 (mp) REVERT: D 34 SER cc_start: 0.8773 (p) cc_final: 0.8518 (m) REVERT: K 10 GLN cc_start: 0.7400 (tt0) cc_final: 0.6490 (pm20) outliers start: 9 outliers final: 3 residues processed: 76 average time/residue: 0.1313 time to fit residues: 12.1585 Evaluate side-chains 62 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 2 CYS Chi-restraints excluded: chain E residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 18 HIS ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 22 ASN C 22 ASN D 22 ASN E 22 ASN F 18 HIS F 22 ASN I 18 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2994 Z= 0.391 Angle : 0.713 6.395 4068 Z= 0.378 Chirality : 0.049 0.143 492 Planarity : 0.003 0.021 534 Dihedral : 7.923 31.846 432 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.94 % Allowed : 14.51 % Favored : 80.56 % 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: -4.63 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 18 PHE 0.019 0.003 PHE I 15 ARG 0.003 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.331 Fit side-chains REVERT: B 27 LEU cc_start: 0.7301 (tt) cc_final: 0.6900 (mp) REVERT: D 27 LEU cc_start: 0.7318 (tt) cc_final: 0.6881 (mp) REVERT: K 10 GLN cc_start: 0.7561 (tt0) cc_final: 0.6525 (tm-30) outliers start: 16 outliers final: 12 residues processed: 59 average time/residue: 0.1410 time to fit residues: 10.1171 Evaluate side-chains 61 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2994 Z= 0.274 Angle : 0.645 6.613 4068 Z= 0.332 Chirality : 0.045 0.133 492 Planarity : 0.002 0.016 534 Dihedral : 7.443 29.651 432 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.09 % Allowed : 19.75 % Favored : 77.16 % 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: -4.56 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.015 0.002 PHE B 23 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.381 Fit side-chains REVERT: B 27 LEU cc_start: 0.7333 (tt) cc_final: 0.6928 (mp) REVERT: D 27 LEU cc_start: 0.7317 (tt) cc_final: 0.6854 (mp) REVERT: F 15 PHE cc_start: 0.7772 (m-80) cc_final: 0.6624 (p90) REVERT: I 11 ARG cc_start: 0.7160 (mtp-110) cc_final: 0.6897 (mmt-90) REVERT: K 10 GLN cc_start: 0.7507 (tt0) cc_final: 0.6668 (tm-30) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.1366 time to fit residues: 10.4143 Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.0470 chunk 17 optimal weight: 4.9990 overall best weight: 2.0318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN C 18 HIS D 18 HIS K 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2994 Z= 0.309 Angle : 0.673 7.789 4068 Z= 0.347 Chirality : 0.045 0.137 492 Planarity : 0.002 0.013 534 Dihedral : 7.488 31.501 432 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.01 % Allowed : 20.06 % Favored : 75.93 % 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: -4.45 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 18 PHE 0.015 0.002 PHE I 15 ARG 0.003 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.333 Fit side-chains REVERT: B 15 PHE cc_start: 0.7792 (m-80) cc_final: 0.7381 (m-80) REVERT: B 27 LEU cc_start: 0.7455 (tt) cc_final: 0.7003 (mp) REVERT: F 15 PHE cc_start: 0.7680 (m-80) cc_final: 0.6645 (p90) REVERT: K 10 GLN cc_start: 0.7535 (tt0) cc_final: 0.6766 (tm-30) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1555 time to fit residues: 9.9684 Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2994 Z= 0.262 Angle : 0.641 8.172 4068 Z= 0.327 Chirality : 0.044 0.133 492 Planarity : 0.002 0.010 534 Dihedral : 7.182 29.976 432 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.32 % Allowed : 22.53 % Favored : 73.15 % 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: -4.46 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.014 0.002 PHE D 23 ARG 0.003 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.333 Fit side-chains REVERT: B 15 PHE cc_start: 0.7807 (m-80) cc_final: 0.7306 (m-80) REVERT: B 27 LEU cc_start: 0.7462 (tt) cc_final: 0.6967 (mp) REVERT: D 27 LEU cc_start: 0.7144 (tt) cc_final: 0.6733 (mp) REVERT: F 15 PHE cc_start: 0.7836 (m-80) cc_final: 0.6815 (p90) outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.0987 time to fit residues: 6.4486 Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2994 Z= 0.200 Angle : 0.573 7.023 4068 Z= 0.292 Chirality : 0.043 0.127 492 Planarity : 0.002 0.009 534 Dihedral : 6.745 26.755 432 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.09 % Allowed : 22.84 % Favored : 74.07 % 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: -4.43 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 18 PHE 0.014 0.002 PHE D 23 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.550 Fit side-chains REVERT: B 15 PHE cc_start: 0.7657 (m-80) cc_final: 0.7115 (m-80) REVERT: B 27 LEU cc_start: 0.7431 (tt) cc_final: 0.6920 (mp) REVERT: F 15 PHE cc_start: 0.7538 (m-80) cc_final: 0.6682 (p90) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.1015 time to fit residues: 6.2621 Evaluate side-chains 50 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 21 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2994 Z= 0.460 Angle : 0.733 7.173 4068 Z= 0.393 Chirality : 0.049 0.148 492 Planarity : 0.003 0.012 534 Dihedral : 8.105 37.434 432 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 4.94 % Allowed : 20.68 % Favored : 74.38 % 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: -4.44 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS J 18 PHE 0.023 0.003 PHE I 15 ARG 0.005 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.342 Fit side-chains REVERT: A 27 LEU cc_start: 0.7306 (tt) cc_final: 0.7044 (mp) REVERT: B 15 PHE cc_start: 0.7595 (m-80) cc_final: 0.7140 (m-80) REVERT: B 27 LEU cc_start: 0.7554 (tt) cc_final: 0.7041 (mp) REVERT: C 15 PHE cc_start: 0.7839 (m-80) cc_final: 0.6619 (p90) REVERT: D 27 LEU cc_start: 0.7260 (tt) cc_final: 0.6843 (mp) outliers start: 16 outliers final: 11 residues processed: 48 average time/residue: 0.0857 time to fit residues: 5.6868 Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2994 Z= 0.174 Angle : 0.590 9.117 4068 Z= 0.292 Chirality : 0.043 0.124 492 Planarity : 0.002 0.008 534 Dihedral : 6.678 25.437 432 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.09 % Allowed : 22.53 % Favored : 74.38 % 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 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.014 0.002 PHE D 23 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.344 Fit side-chains REVERT: B 15 PHE cc_start: 0.7399 (m-80) cc_final: 0.7064 (m-80) REVERT: B 27 LEU cc_start: 0.7492 (tt) cc_final: 0.7009 (mp) REVERT: C 15 PHE cc_start: 0.7649 (m-80) cc_final: 0.6344 (p90) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.1121 time to fit residues: 6.5163 Evaluate side-chains 48 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 0.0040 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.7544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2994 Z= 0.159 Angle : 0.572 8.709 4068 Z= 0.282 Chirality : 0.042 0.121 492 Planarity : 0.001 0.008 534 Dihedral : 6.402 23.959 432 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.47 % Allowed : 23.46 % Favored : 74.07 % 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: -4.43 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.013 0.001 PHE D 23 ARG 0.002 0.000 ARG F 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.303 Fit side-chains REVERT: B 15 PHE cc_start: 0.7398 (m-80) cc_final: 0.7007 (m-80) REVERT: B 27 LEU cc_start: 0.7468 (tt) cc_final: 0.6997 (mp) REVERT: C 15 PHE cc_start: 0.7607 (m-80) cc_final: 0.6295 (p90) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.1387 time to fit residues: 8.0386 Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.149553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.116996 restraints weight = 4870.183| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.18 r_work: 0.3818 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2994 Z= 0.184 Angle : 0.597 8.970 4068 Z= 0.290 Chirality : 0.042 0.126 492 Planarity : 0.002 0.007 534 Dihedral : 6.582 26.574 432 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.47 % Allowed : 23.77 % Favored : 73.77 % 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: -4.36 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.014 0.002 PHE D 23 ARG 0.002 0.000 ARG F 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1104.10 seconds wall clock time: 20 minutes 42.88 seconds (1242.88 seconds total)