Starting phenix.real_space_refine on Thu Dec 7 15:49:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/12_2023/7m64_23688_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/12_2023/7m64_23688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/12_2023/7m64_23688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/12_2023/7m64_23688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/12_2023/7m64_23688_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/12_2023/7m64_23688_updated.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 1.000 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: 3 Type Number sf(0) Gaussians C 1140 2.51 5 N 330 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1850 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "F" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "G" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "J" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Time building chain proxies: 1.48, per 1000 atoms: 0.80 Number of scatterers: 1850 At special positions: 0 Unit cell: (48.53, 66.465, 44.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 380 8.00 N 330 7.00 C 1140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 356.4 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 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: 0.36 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: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 300 1.29 - 1.36: 323 1.36 - 1.43: 267 1.43 - 1.50: 297 1.50 - 1.56: 693 Bond restraints: 1880 Sorted by residual: bond pdb=" C TYR D 37 " pdb=" N NH2 D 38 " ideal model delta sigma weight residual 2.329 1.327 1.002 1.40e-02 5.10e+03 5.13e+03 bond pdb=" C TYR B 37 " pdb=" N NH2 B 38 " ideal model delta sigma weight residual 2.329 1.327 1.002 1.40e-02 5.10e+03 5.12e+03 bond pdb=" C TYR I 37 " pdb=" N NH2 I 38 " ideal model delta sigma weight residual 2.329 1.327 1.002 1.40e-02 5.10e+03 5.12e+03 bond pdb=" C TYR G 37 " pdb=" N NH2 G 38 " ideal model delta sigma weight residual 2.329 1.327 1.002 1.40e-02 5.10e+03 5.12e+03 bond pdb=" C TYR C 37 " pdb=" N NH2 C 38 " ideal model delta sigma weight residual 2.329 1.327 1.002 1.40e-02 5.10e+03 5.12e+03 ... (remaining 1875 not shown) Histogram of bond angle deviations from ideal: 105.94 - 110.97: 691 110.97 - 116.01: 554 116.01 - 121.04: 672 121.04 - 126.08: 633 126.08 - 131.12: 10 Bond angle restraints: 2560 Sorted by residual: angle pdb=" C ALA H 13 " pdb=" CA ALA H 13 " pdb=" CB ALA H 13 " ideal model delta sigma weight residual 110.50 116.35 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta sigma weight residual 110.50 116.34 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA B 13 " pdb=" CA ALA B 13 " pdb=" CB ALA B 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA F 13 " pdb=" CA ALA F 13 " pdb=" CB ALA F 13 " ideal model delta sigma weight residual 110.50 116.32 -5.82 1.50e+00 4.44e-01 1.51e+01 ... (remaining 2555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.60: 760 5.60 - 11.20: 140 11.20 - 16.80: 59 16.80 - 22.40: 61 22.40 - 27.99: 20 Dihedral angle restraints: 1040 sinusoidal: 330 harmonic: 710 Sorted by residual: dihedral pdb=" C ALA J 13 " pdb=" N ALA J 13 " pdb=" CA ALA J 13 " pdb=" CB ALA J 13 " ideal model delta harmonic sigma weight residual -122.60 -132.53 9.93 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" C ALA C 13 " pdb=" N ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta harmonic sigma weight residual -122.60 -132.51 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C ALA E 13 " pdb=" N ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta harmonic sigma weight residual -122.60 -132.49 9.89 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 1037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 224 0.045 - 0.090: 36 0.090 - 0.135: 11 0.135 - 0.179: 9 0.179 - 0.224: 20 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ALA J 13 " pdb=" N ALA J 13 " pdb=" C ALA J 13 " pdb=" CB ALA J 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA C 13 " pdb=" N ALA C 13 " pdb=" C ALA C 13 " pdb=" CB ALA C 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA G 13 " pdb=" N ALA G 13 " pdb=" C ALA G 13 " pdb=" CB ALA G 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 297 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 13 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA F 13 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA F 13 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN F 14 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 13 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA C 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 13 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA H 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA H 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN H 14 " -0.008 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 998 2.94 - 3.43: 2268 3.43 - 3.92: 2957 3.92 - 4.41: 3341 4.41 - 4.90: 6391 Nonbonded interactions: 15955 Sorted by model distance: nonbonded pdb=" OG SER I 19 " pdb=" OD1 ASN I 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER A 19 " pdb=" OD1 ASN A 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.451 2.440 ... (remaining 15950 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.080 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: 0.550 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.073 1.002 1880 Z= 5.237 Angle : 1.151 5.847 2560 Z= 0.674 Chirality : 0.068 0.224 300 Planarity : 0.004 0.013 340 Dihedral : 10.068 27.994 580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.40), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 18 PHE 0.009 0.002 PHE F 23 TYR 0.003 0.001 TYR F 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0712 time to fit residues: 2.9501 Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2416 ------------------------------------------------------------------------------- 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: 8.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1880 Z= 0.224 Angle : 0.845 6.632 2560 Z= 0.425 Chirality : 0.046 0.123 300 Planarity : 0.002 0.008 340 Dihedral : 4.685 12.532 250 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 11.43 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.38), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.29), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS J 18 PHE 0.013 0.002 PHE H 23 TYR 0.006 0.002 TYR J 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.221 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0699 time to fit residues: 2.2819 Evaluate side-chains 24 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.221 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0229 time to fit residues: 0.3375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 2 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1880 Z= 0.186 Angle : 0.783 7.156 2560 Z= 0.391 Chirality : 0.045 0.131 300 Planarity : 0.002 0.008 340 Dihedral : 4.629 12.192 250 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.38), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.29), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.008 0.002 PHE A 15 TYR 0.006 0.001 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0710 time to fit residues: 2.0589 Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1880 Z= 0.230 Angle : 0.804 6.784 2560 Z= 0.408 Chirality : 0.045 0.137 300 Planarity : 0.002 0.010 340 Dihedral : 4.787 12.246 250 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.90 % Allowed : 13.81 % Favored : 84.29 % 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: -3.96 (0.38), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.29), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.009 0.002 PHE H 23 TYR 0.008 0.002 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.223 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.0698 time to fit residues: 2.0253 Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.221 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0249 time to fit residues: 0.3577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1880 Z= 0.152 Angle : 0.745 8.527 2560 Z= 0.364 Chirality : 0.044 0.132 300 Planarity : 0.002 0.011 340 Dihedral : 4.571 11.515 250 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.95 % Allowed : 15.71 % Favored : 83.33 % 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: -4.07 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.006 0.002 PHE E 15 TYR 0.004 0.001 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.223 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.0683 time to fit residues: 2.0227 Evaluate side-chains 16 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN I 35 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1880 Z= 0.178 Angle : 0.764 6.950 2560 Z= 0.377 Chirality : 0.044 0.133 300 Planarity : 0.002 0.011 340 Dihedral : 4.626 11.799 250 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 17.14 % Favored : 81.90 % 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: -4.00 (0.38), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.29), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 18 PHE 0.007 0.002 PHE E 15 TYR 0.005 0.001 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.233 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 17 average time/residue: 0.0696 time to fit residues: 1.8072 Evaluate side-chains 14 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN I 35 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1880 Z= 0.136 Angle : 0.766 8.756 2560 Z= 0.362 Chirality : 0.043 0.129 300 Planarity : 0.002 0.010 340 Dihedral : 4.449 11.635 250 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.43 % Allowed : 17.62 % Favored : 80.95 % 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: -4.05 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.006 0.001 PHE A 23 TYR 0.003 0.000 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.226 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 18 average time/residue: 0.0678 time to fit residues: 1.8438 Evaluate side-chains 15 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 0.0170 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 overall best weight: 4.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1880 Z= 0.135 Angle : 0.753 7.703 2560 Z= 0.359 Chirality : 0.043 0.126 300 Planarity : 0.002 0.010 340 Dihedral : 4.341 12.147 250 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 18.10 % Favored : 81.43 % 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: -4.09 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 18 PHE 0.006 0.001 PHE H 23 TYR 0.003 0.000 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.222 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0645 time to fit residues: 1.9309 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 0.0060 chunk 2 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 overall best weight: 11.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN I 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1880 Z= 0.256 Angle : 0.861 7.923 2560 Z= 0.429 Chirality : 0.045 0.137 300 Planarity : 0.003 0.014 340 Dihedral : 4.942 14.251 250 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.95 % Allowed : 18.10 % Favored : 80.95 % 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: -4.06 (0.38), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.29), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS J 18 PHE 0.012 0.002 PHE H 23 TYR 0.007 0.001 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.167 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 19 average time/residue: 0.0555 time to fit residues: 1.5353 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN I 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1880 Z= 0.195 Angle : 0.829 8.227 2560 Z= 0.396 Chirality : 0.043 0.129 300 Planarity : 0.002 0.012 340 Dihedral : 4.765 13.524 250 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.48 % Allowed : 16.67 % Favored : 82.86 % 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: -4.12 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 18 PHE 0.006 0.002 PHE H 23 TYR 0.009 0.001 TYR I 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.262 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0710 time to fit residues: 1.8649 Evaluate side-chains 16 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0254 time to fit residues: 0.3416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.099030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.088838 restraints weight = 6305.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.090741 restraints weight = 3346.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.091992 restraints weight = 2104.354| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1880 Z= 0.164 Angle : 0.831 8.238 2560 Z= 0.386 Chirality : 0.044 0.130 300 Planarity : 0.002 0.011 340 Dihedral : 4.635 13.191 250 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.48 % Allowed : 17.14 % Favored : 82.38 % 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: -4.10 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.006 0.002 PHE A 23 TYR 0.003 0.001 TYR I 37 =============================================================================== Job complete usr+sys time: 657.39 seconds wall clock time: 18 minutes 23.61 seconds (1103.61 seconds total)