Starting phenix.real_space_refine on Mon Sep 23 11:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/09_2024/6vw2_21410.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/09_2024/6vw2_21410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/09_2024/6vw2_21410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/09_2024/6vw2_21410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/09_2024/6vw2_21410.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/09_2024/6vw2_21410.cif" } resolution = 3.4 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 1110 2.51 5 N 310 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1800 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 180 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 0.76, per 1000 atoms: 0.42 Number of scatterers: 1800 At special positions: 0 Unit cell: (50.008, 75.544, 39.368, 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 310 7.00 C 1110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 222.4 milliseconds 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 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 6 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 15 through 16 removed outlier: 5.819A pdb=" N PHE A 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE E 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 22 through 23 removed outlier: 7.473A pdb=" N ASN D 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN A 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 26 through 32 removed outlier: 6.927A pdb=" N SER D 29 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR H 30 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER A 29 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR D 30 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 26 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER E 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER A 28 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ASN E 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR A 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE E 26 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER I 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N SER E 28 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ASN I 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR E 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 15 through 16 removed outlier: 5.808A pdb=" N PHE C 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE B 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 22 through 23 removed outlier: 7.460A pdb=" N ASN B 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN F 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 26 through 32 removed outlier: 6.870A pdb=" N ILE C 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER G 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N SER C 28 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ASN G 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR C 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 26 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER C 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER B 28 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ASN C 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER B 29 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR F 30 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER F 29 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR J 30 " --> pdb=" O SER F 29 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 0.42 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 300 1.28 - 1.35: 300 1.35 - 1.41: 240 1.41 - 1.47: 290 1.47 - 1.54: 700 Bond restraints: 1830 Sorted by residual: bond pdb=" CA SER G 20 " pdb=" C SER G 20 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.32e-02 5.74e+03 1.08e+00 bond pdb=" CA SER E 20 " pdb=" C SER E 20 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.32e-02 5.74e+03 1.06e+00 bond pdb=" CA SER J 20 " pdb=" C SER J 20 " ideal model delta sigma weight residual 1.528 1.514 0.013 1.32e-02 5.74e+03 1.05e+00 bond pdb=" CA SER H 20 " pdb=" C SER H 20 " ideal model delta sigma weight residual 1.528 1.515 0.013 1.32e-02 5.74e+03 1.00e+00 bond pdb=" CA SER C 20 " pdb=" C SER C 20 " ideal model delta sigma weight residual 1.528 1.515 0.013 1.32e-02 5.74e+03 9.91e-01 ... (remaining 1825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 2050 1.28 - 2.56: 320 2.56 - 3.84: 90 3.84 - 5.13: 20 5.13 - 6.41: 10 Bond angle restraints: 2490 Sorted by residual: angle pdb=" C SER B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 122.35 127.41 -5.06 1.46e+00 4.69e-01 1.20e+01 angle pdb=" C SER J 19 " pdb=" N SER J 20 " pdb=" CA SER J 20 " ideal model delta sigma weight residual 122.35 127.41 -5.06 1.46e+00 4.69e-01 1.20e+01 angle pdb=" C SER I 19 " pdb=" N SER I 20 " pdb=" CA SER I 20 " ideal model delta sigma weight residual 122.35 127.40 -5.05 1.46e+00 4.69e-01 1.20e+01 angle pdb=" C SER D 19 " pdb=" N SER D 20 " pdb=" CA SER D 20 " ideal model delta sigma weight residual 122.35 127.40 -5.05 1.46e+00 4.69e-01 1.19e+01 angle pdb=" C SER G 19 " pdb=" N SER G 20 " pdb=" CA SER G 20 " ideal model delta sigma weight residual 122.35 127.39 -5.04 1.46e+00 4.69e-01 1.19e+01 ... (remaining 2485 not shown) Histogram of dihedral angle deviations from ideal: 0.08 - 7.54: 700 7.54 - 14.99: 140 14.99 - 22.45: 100 22.45 - 29.90: 60 29.90 - 37.36: 20 Dihedral angle restraints: 1020 sinusoidal: 340 harmonic: 680 Sorted by residual: dihedral pdb=" CA ALA G 25 " pdb=" C ALA G 25 " pdb=" N ILE G 26 " pdb=" CA ILE G 26 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ALA I 25 " pdb=" C ALA I 25 " pdb=" N ILE I 26 " pdb=" CA ILE I 26 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 1017 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.030: 132 0.030 - 0.059: 58 0.059 - 0.087: 60 0.087 - 0.116: 10 0.116 - 0.144: 30 Chirality restraints: 290 Sorted by residual: chirality pdb=" CG LEU C 27 " pdb=" CB LEU C 27 " pdb=" CD1 LEU C 27 " pdb=" CD2 LEU C 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CG LEU G 27 " pdb=" CB LEU G 27 " pdb=" CD1 LEU G 27 " pdb=" CD2 LEU G 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA SER J 20 " pdb=" N SER J 20 " pdb=" C SER J 20 " pdb=" CB SER J 20 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 287 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 36 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C THR G 36 " -0.060 2.00e-02 2.50e+03 pdb=" O THR G 36 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR G 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C THR E 36 " 0.060 2.00e-02 2.50e+03 pdb=" O THR E 36 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 37 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 36 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C THR D 36 " 0.060 2.00e-02 2.50e+03 pdb=" O THR D 36 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR D 37 " -0.020 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 618 2.81 - 3.34: 1772 3.34 - 3.86: 3038 3.86 - 4.38: 3852 4.38 - 4.90: 6750 Nonbonded interactions: 16030 Sorted by model distance: nonbonded pdb=" O SER D 20 " pdb=" OG SER D 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER F 20 " pdb=" OG SER F 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER H 20 " pdb=" OG SER H 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER E 20 " pdb=" OG SER E 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER A 20 " pdb=" OG SER A 20 " model vdw 2.293 3.040 ... (remaining 16025 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: 0.010 Normalize map: mean=0, sd=1: 0.110 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: 0.010 Set scattering table: 0.030 Process input model: 9.220 Find NCS groups from input model: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.006 0.024 1830 Z= 0.434 Angle : 1.134 6.407 2490 Z= 0.640 Chirality : 0.062 0.144 290 Planarity : 0.012 0.035 330 Dihedral : 14.199 37.360 580 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.27 % Favored : 72.73 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.32), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.010 HIS D 18 PHE 0.016 0.004 PHE D 23 TYR 0.004 0.002 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.197 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0580 time to fit residues: 1.9752 Evaluate side-chains 23 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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: 9.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 1830 Z= 0.238 Angle : 0.727 5.540 2490 Z= 0.407 Chirality : 0.050 0.148 290 Planarity : 0.003 0.009 330 Dihedral : 10.212 39.167 250 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.82 % Favored : 78.18 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % 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: -4.56 (0.39), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.30), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS D 18 PHE 0.009 0.002 PHE E 23 TYR 0.006 0.002 TYR J 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.207 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.0686 time to fit residues: 2.9817 Evaluate side-chains 33 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain I residue 22 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 1830 Z= 0.464 Angle : 0.975 5.846 2490 Z= 0.546 Chirality : 0.058 0.177 290 Planarity : 0.003 0.012 330 Dihedral : 11.897 45.927 250 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.36 % Favored : 78.64 % Rotamer: Outliers : 5.24 % Allowed : 31.43 % Favored : 63.33 % 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: -4.47 (0.42), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.32), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.006 HIS F 18 PHE 0.008 0.002 PHE H 15 TYR 0.007 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.194 Fit side-chains REVERT: A 35 ASN cc_start: 0.8164 (p0) cc_final: 0.7962 (p0) REVERT: B 14 ASN cc_start: 0.6658 (t0) cc_final: 0.6397 (t0) REVERT: B 35 ASN cc_start: 0.8089 (p0) cc_final: 0.7459 (p0) REVERT: C 35 ASN cc_start: 0.8122 (p0) cc_final: 0.7821 (p0) REVERT: D 35 ASN cc_start: 0.7959 (p0) cc_final: 0.7300 (p0) REVERT: F 35 ASN cc_start: 0.8038 (p0) cc_final: 0.7736 (p0) REVERT: H 15 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: I 35 ASN cc_start: 0.8401 (p0) cc_final: 0.8196 (p0) REVERT: J 35 ASN cc_start: 0.8187 (p0) cc_final: 0.7663 (p0) outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 0.0657 time to fit residues: 4.3945 Evaluate side-chains 49 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 15 PHE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1830 Z= 0.210 Angle : 0.701 4.819 2490 Z= 0.394 Chirality : 0.047 0.151 290 Planarity : 0.002 0.008 330 Dihedral : 9.769 40.796 250 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.33 % Allowed : 30.00 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.40), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.30), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS A 18 PHE 0.007 0.001 PHE J 15 TYR 0.004 0.001 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.178 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 0.0674 time to fit residues: 3.4213 Evaluate side-chains 37 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1830 Z= 0.348 Angle : 0.831 5.515 2490 Z= 0.466 Chirality : 0.053 0.172 290 Planarity : 0.003 0.010 330 Dihedral : 10.763 43.333 250 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 6.19 % Allowed : 32.86 % Favored : 60.95 % 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: -4.83 (0.38), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS A 18 PHE 0.006 0.002 PHE E 23 TYR 0.006 0.002 TYR A 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.209 Fit side-chains REVERT: A 15 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: F 35 ASN cc_start: 0.8031 (p0) cc_final: 0.7707 (p0) REVERT: H 35 ASN cc_start: 0.8033 (p0) cc_final: 0.7756 (p0) outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 0.0722 time to fit residues: 4.4012 Evaluate side-chains 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1830 Z= 0.297 Angle : 0.791 6.578 2490 Z= 0.442 Chirality : 0.050 0.169 290 Planarity : 0.002 0.009 330 Dihedral : 10.278 42.540 250 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 6.19 % Allowed : 34.29 % Favored : 59.52 % 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: -4.95 (0.38), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS A 18 PHE 0.006 0.002 PHE H 15 TYR 0.005 0.001 TYR A 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.186 Fit side-chains REVERT: A 15 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: F 35 ASN cc_start: 0.8016 (p0) cc_final: 0.7697 (p0) outliers start: 13 outliers final: 9 residues processed: 42 average time/residue: 0.0669 time to fit residues: 3.6852 Evaluate side-chains 41 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1830 Z= 0.267 Angle : 0.753 6.647 2490 Z= 0.419 Chirality : 0.049 0.166 290 Planarity : 0.002 0.008 330 Dihedral : 9.968 41.544 250 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 6.67 % Allowed : 34.76 % Favored : 58.57 % 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: -5.08 (0.36), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS A 18 PHE 0.005 0.001 PHE E 23 TYR 0.005 0.001 TYR A 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 0.199 Fit side-chains REVERT: A 15 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: B 18 HIS cc_start: 0.6375 (OUTLIER) cc_final: 0.5970 (p-80) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.0676 time to fit residues: 3.9278 Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU 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: 9.9990 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1830 Z= 0.307 Angle : 0.790 6.776 2490 Z= 0.440 Chirality : 0.051 0.163 290 Planarity : 0.002 0.010 330 Dihedral : 10.211 42.046 250 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 5.71 % Allowed : 35.24 % Favored : 59.05 % 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: -5.16 (0.37), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS A 18 PHE 0.006 0.002 PHE H 15 TYR 0.006 0.001 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.198 Fit side-chains REVERT: A 15 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7494 (m-10) REVERT: B 18 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5997 (p-80) REVERT: F 35 ASN cc_start: 0.8026 (p0) cc_final: 0.7726 (p0) outliers start: 12 outliers final: 9 residues processed: 44 average time/residue: 0.0561 time to fit residues: 3.3089 Evaluate side-chains 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 0.1980 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1830 Z= 0.223 Angle : 0.705 6.667 2490 Z= 0.392 Chirality : 0.047 0.157 290 Planarity : 0.002 0.008 330 Dihedral : 9.474 39.350 250 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 4.76 % Allowed : 36.67 % Favored : 58.57 % 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: -5.20 (0.36), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS A 18 PHE 0.005 0.001 PHE J 15 TYR 0.004 0.001 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.221 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 0.0680 time to fit residues: 3.9418 Evaluate side-chains 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU 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: 20.0000 chunk 13 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1830 Z= 0.286 Angle : 0.764 6.631 2490 Z= 0.426 Chirality : 0.050 0.162 290 Planarity : 0.002 0.010 330 Dihedral : 9.942 40.907 250 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 4.29 % Allowed : 35.71 % Favored : 60.00 % 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: -5.23 (0.36), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS B 18 PHE 0.005 0.002 PHE E 23 TYR 0.006 0.001 TYR A 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.229 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 42 average time/residue: 0.0594 time to fit residues: 3.3395 Evaluate side-chains 43 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 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 = 0.4432 r_free = 0.4432 target = 0.134427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.115604 restraints weight = 2810.046| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.38 r_work: 0.4045 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1830 Z= 0.306 Angle : 0.789 6.689 2490 Z= 0.439 Chirality : 0.051 0.166 290 Planarity : 0.002 0.011 330 Dihedral : 10.121 41.191 250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 4.76 % Allowed : 35.24 % Favored : 60.00 % 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: -5.26 (0.36), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS B 18 PHE 0.005 0.002 PHE H 15 TYR 0.006 0.002 TYR I 37 =============================================================================== Job complete usr+sys time: 715.88 seconds wall clock time: 18 minutes 24.39 seconds (1104.39 seconds total)