Starting phenix.real_space_refine on Mon Sep 23 11:43:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az1_15729/09_2024/8az1_15729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az1_15729/09_2024/8az1_15729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az1_15729/09_2024/8az1_15729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az1_15729/09_2024/8az1_15729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az1_15729/09_2024/8az1_15729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az1_15729/09_2024/8az1_15729.cif" } resolution = 3.1 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: 3 Type Number sf(0) Gaussians C 1130 2.51 5 N 330 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 0.83, per 1000 atoms: 0.45 Number of scatterers: 1830 At special positions: 0 Unit cell: (38.64, 86.52, 38.64, 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 370 8.00 N 330 7.00 C 1130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 237.5 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: 440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.460A pdb=" N ASN A 22 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 22 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN E 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN G 22 " --> pdb=" O PHE I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 8.551A pdb=" N THR A 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR C 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR E 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR G 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.442A pdb=" N ASN B 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN F 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN H 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 8.566A pdb=" N THR B 30 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR D 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR F 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR H 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 36 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 300 1.29 - 1.35: 311 1.35 - 1.41: 228 1.41 - 1.48: 301 1.48 - 1.54: 710 Bond restraints: 1850 Sorted by residual: bond pdb=" C GLY H 33 " pdb=" O GLY H 33 " ideal model delta sigma weight residual 1.238 1.231 0.006 1.12e-02 7.97e+03 3.34e-01 bond pdb=" C GLY A 20 " pdb=" O GLY A 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 3.07e-01 bond pdb=" C GLY E 20 " pdb=" O GLY E 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 3.04e-01 bond pdb=" C GLY J 33 " pdb=" O GLY J 33 " ideal model delta sigma weight residual 1.238 1.231 0.006 1.12e-02 7.97e+03 2.93e-01 bond pdb=" C GLY I 20 " pdb=" O GLY I 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 2.85e-01 ... (remaining 1845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 2341 0.85 - 1.70: 124 1.70 - 2.55: 25 2.55 - 3.40: 0 3.40 - 4.25: 20 Bond angle restraints: 2510 Sorted by residual: angle pdb=" N GLY B 20 " pdb=" CA GLY B 20 " pdb=" C GLY B 20 " ideal model delta sigma weight residual 113.48 117.73 -4.25 1.46e+00 4.69e-01 8.49e+00 angle pdb=" N GLY I 20 " pdb=" CA GLY I 20 " pdb=" C GLY I 20 " ideal model delta sigma weight residual 113.48 117.71 -4.23 1.46e+00 4.69e-01 8.38e+00 angle pdb=" N GLY D 20 " pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 113.48 117.70 -4.22 1.46e+00 4.69e-01 8.35e+00 angle pdb=" N GLY C 20 " pdb=" CA GLY C 20 " pdb=" C GLY C 20 " ideal model delta sigma weight residual 113.48 117.67 -4.19 1.46e+00 4.69e-01 8.24e+00 angle pdb=" N GLY A 20 " pdb=" CA GLY A 20 " pdb=" C GLY A 20 " ideal model delta sigma weight residual 113.48 117.65 -4.17 1.46e+00 4.69e-01 8.17e+00 ... (remaining 2505 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 7.64: 820 7.64 - 15.28: 110 15.28 - 22.91: 40 22.91 - 30.55: 30 30.55 - 38.18: 10 Dihedral angle restraints: 1010 sinusoidal: 320 harmonic: 690 Sorted by residual: dihedral pdb=" N HIS A 18 " pdb=" CA HIS A 18 " pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.82 -38.18 3 1.50e+01 4.44e-03 6.71e+00 dihedral pdb=" N HIS G 18 " pdb=" CA HIS G 18 " pdb=" CB HIS G 18 " pdb=" CG HIS G 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.89 -38.11 3 1.50e+01 4.44e-03 6.69e+00 dihedral pdb=" N HIS C 18 " pdb=" CA HIS C 18 " pdb=" CB HIS C 18 " pdb=" CG HIS C 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.89 -38.11 3 1.50e+01 4.44e-03 6.69e+00 ... (remaining 1007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 160 0.024 - 0.047: 74 0.047 - 0.071: 26 0.071 - 0.094: 15 0.094 - 0.118: 15 Chirality restraints: 290 Sorted by residual: chirality pdb=" CA ILE E 26 " pdb=" N ILE E 26 " pdb=" C ILE E 26 " pdb=" CB ILE E 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 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 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE J 26 " pdb=" N ILE J 26 " pdb=" C ILE J 26 " pdb=" CB ILE J 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 287 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 28 " -0.004 2.00e-02 2.50e+03 7.26e-03 5.27e-01 pdb=" C SER F 28 " 0.013 2.00e-02 2.50e+03 pdb=" O SER F 28 " -0.005 2.00e-02 2.50e+03 pdb=" N SER F 29 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 28 " -0.004 2.00e-02 2.50e+03 7.25e-03 5.26e-01 pdb=" C SER D 28 " 0.013 2.00e-02 2.50e+03 pdb=" O SER D 28 " -0.005 2.00e-02 2.50e+03 pdb=" N SER D 29 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 28 " 0.004 2.00e-02 2.50e+03 7.11e-03 5.06e-01 pdb=" C SER I 28 " -0.012 2.00e-02 2.50e+03 pdb=" O SER I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N SER I 29 " 0.004 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 757 2.88 - 3.38: 1501 3.38 - 3.89: 3175 3.89 - 4.39: 3586 4.39 - 4.90: 7029 Nonbonded interactions: 16048 Sorted by model distance: nonbonded pdb=" O SER A 19 " pdb=" ND2 ASN A 21 " model vdw 2.374 3.120 nonbonded pdb=" O SER G 19 " pdb=" ND2 ASN G 21 " model vdw 2.374 3.120 nonbonded pdb=" O SER J 19 " pdb=" ND2 ASN J 21 " model vdw 2.375 3.120 nonbonded pdb=" O SER E 19 " pdb=" ND2 ASN E 21 " model vdw 2.375 3.120 nonbonded pdb=" O SER C 19 " pdb=" ND2 ASN C 21 " model vdw 2.375 3.120 ... (remaining 16043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.004 0.017 1850 Z= 0.256 Angle : 0.577 4.255 2510 Z= 0.355 Chirality : 0.041 0.118 290 Planarity : 0.002 0.007 330 Dihedral : 10.899 38.181 570 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.002 0.001 PHE F 23 TYR 0.001 0.001 TYR H 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 11 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0871 time to fit residues: 1.4458 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1850 Z= 0.238 Angle : 0.483 2.852 2510 Z= 0.281 Chirality : 0.044 0.124 290 Planarity : 0.002 0.005 330 Dihedral : 4.277 12.740 250 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.005 0.001 PHE C 23 TYR 0.006 0.001 TYR A 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0886 time to fit residues: 1.3552 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** ** C 35 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** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1850 Z= 0.222 Angle : 0.462 2.756 2510 Z= 0.271 Chirality : 0.044 0.122 290 Planarity : 0.002 0.004 330 Dihedral : 4.300 13.313 250 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 18 PHE 0.005 0.001 PHE I 15 TYR 0.008 0.002 TYR I 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0901 time to fit residues: 1.3687 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 35 ASN C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 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 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1850 Z= 0.276 Angle : 0.472 2.948 2510 Z= 0.281 Chirality : 0.045 0.123 290 Planarity : 0.002 0.005 330 Dihedral : 4.702 14.836 250 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 18 PHE 0.006 0.001 PHE C 23 TYR 0.008 0.002 TYR C 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0934 time to fit residues: 1.4228 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN J 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1850 Z= 0.412 Angle : 0.517 3.280 2510 Z= 0.310 Chirality : 0.047 0.122 290 Planarity : 0.002 0.006 330 Dihedral : 5.178 16.171 250 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 18 PHE 0.008 0.002 PHE C 23 TYR 0.012 0.002 TYR E 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1065 time to fit residues: 1.6207 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 1850 Z= 0.352 Angle : 0.495 3.162 2510 Z= 0.297 Chirality : 0.046 0.123 290 Planarity : 0.002 0.006 330 Dihedral : 5.002 15.900 250 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS F 18 PHE 0.007 0.001 PHE C 23 TYR 0.010 0.002 TYR C 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1278 time to fit residues: 1.8750 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1850 Z= 0.251 Angle : 0.465 2.901 2510 Z= 0.277 Chirality : 0.045 0.125 290 Planarity : 0.002 0.004 330 Dihedral : 4.624 15.083 250 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.004 0.001 PHE H 23 TYR 0.010 0.002 TYR B 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.150 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0984 time to fit residues: 1.4108 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1850 Z= 0.119 Angle : 0.427 3.155 2510 Z= 0.250 Chirality : 0.044 0.126 290 Planarity : 0.001 0.004 330 Dihedral : 3.907 12.840 250 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.002 0.000 PHE I 15 TYR 0.009 0.001 TYR B 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0943 time to fit residues: 1.6090 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 9.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1850 Z= 0.197 Angle : 0.439 3.120 2510 Z= 0.259 Chirality : 0.044 0.124 290 Planarity : 0.001 0.004 330 Dihedral : 4.230 13.833 250 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 18 PHE 0.003 0.001 PHE H 23 TYR 0.009 0.001 TYR B 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0915 time to fit residues: 1.4002 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 1850 Z= 0.458 Angle : 0.531 3.295 2510 Z= 0.321 Chirality : 0.047 0.120 290 Planarity : 0.002 0.006 330 Dihedral : 5.275 16.982 250 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 18 PHE 0.009 0.002 PHE C 23 TYR 0.013 0.002 TYR B 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 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0858 time to fit residues: 1.3451 Evaluate side-chains 10 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3552 r_free = 0.3552 target = 0.097217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077332 restraints weight = 2922.337| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.06 r_work: 0.3253 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1850 Z= 0.251 Angle : 0.468 3.310 2510 Z= 0.278 Chirality : 0.045 0.126 290 Planarity : 0.002 0.004 330 Dihedral : 4.684 15.477 250 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.004 0.001 PHE H 23 TYR 0.011 0.001 TYR B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 926.03 seconds wall clock time: 21 minutes 34.17 seconds (1294.17 seconds total)