Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/11_2022/6vw2_21410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/11_2022/6vw2_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_21410/11_2022/6vw2_21410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/11_2022/6vw2_21410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/11_2022/6vw2_21410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vw2_21410/11_2022/6vw2_21410.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 1800 Number of models: 1 Model: "" Number of chains: 10 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} Chain: "B" 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} Chain: "C" 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} Chain: "D" 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} Chain: "E" 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} Chain: "F" 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} Chain: "G" 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} Chain: "H" 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} Chain: "I" 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} Chain: "J" 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} Time building chain proxies: 1.60, per 1000 atoms: 0.89 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 316.7 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: 0.18 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: 0.84 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: 105.83 - 110.83: 665 110.83 - 115.83: 514 115.83 - 120.82: 638 120.82 - 125.82: 653 125.82 - 130.82: 20 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 2.440 nonbonded pdb=" O SER F 20 " pdb=" OG SER F 20 " model vdw 2.292 2.440 nonbonded pdb=" O SER H 20 " pdb=" OG SER H 20 " model vdw 2.292 2.440 nonbonded pdb=" O SER E 20 " pdb=" OG SER E 20 " model vdw 2.292 2.440 nonbonded pdb=" O SER A 20 " pdb=" OG SER A 20 " model vdw 2.293 2.440 ... (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 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 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. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.600 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.010 Process input model: 10.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 % 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 *********************** 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 : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0628 time to fit residues: 2.1365 Evaluate side-chains 23 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2721 ------------------------------------------------------------------------------- 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: 0.5980 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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: 0.7134 moved from start: 0.2021 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= 0.212 Angle : 0.653 5.400 2490 Z= 0.356 Chirality : 0.048 0.145 290 Planarity : 0.002 0.008 330 Dihedral : 9.868 37.502 250 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer Outliers : 9.05 % 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: -4.42 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.33), residues: 220 *********************** 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 48 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 29 time to evaluate : 0.192 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 39 average time/residue: 0.0619 time to fit residues: 3.2071 Evaluate side-chains 45 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 29 time to evaluate : 0.188 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0217 time to fit residues: 0.8520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** ** 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: 0.7332 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.030 1830 Z= 0.426 Angle : 0.896 5.980 2490 Z= 0.499 Chirality : 0.056 0.171 290 Planarity : 0.003 0.011 330 Dihedral : 11.678 45.241 250 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % Rotamer Outliers : 8.10 % 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: -4.40 (0.44), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.34), residues: 220 *********************** 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 47 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 30 time to evaluate : 0.211 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 41 average time/residue: 0.0627 time to fit residues: 3.5143 Evaluate side-chains 39 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0231 time to fit residues: 0.6018 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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: 0.7191 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.014 1830 Z= 0.201 Angle : 0.644 5.673 2490 Z= 0.352 Chirality : 0.046 0.147 290 Planarity : 0.002 0.008 330 Dihedral : 9.701 40.299 250 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer Outliers : 6.67 % 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: -4.41 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.33), residues: 220 *********************** 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 41 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.200 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 38 average time/residue: 0.0665 time to fit residues: 3.4148 Evaluate side-chains 36 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0232 time to fit residues: 0.6009 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 overall best weight: 5.7190 ------------------------------------------------------------------------------- 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: 0.7281 moved from start: 0.3066 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= 0.325 Angle : 0.780 6.176 2490 Z= 0.426 Chirality : 0.050 0.167 290 Planarity : 0.002 0.009 330 Dihedral : 10.703 42.872 250 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer Outliers : 9.05 % 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: -4.64 (0.42), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.32), residues: 220 *********************** 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 50 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 31 time to evaluate : 0.203 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 46 average time/residue: 0.0599 time to fit residues: 3.6928 Evaluate side-chains 42 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 28 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0214 time to fit residues: 0.7424 ------------------------------------------------------------------------------- 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: 20.0000 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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** ** 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: 0.7264 moved from start: 0.3231 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= 0.297 Angle : 0.751 6.444 2490 Z= 0.408 Chirality : 0.049 0.168 290 Planarity : 0.002 0.010 330 Dihedral : 10.395 42.339 250 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer Outliers : 7.14 % 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: -4.68 (0.42), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.32), residues: 220 *********************** 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: 15 poor density : 29 time to evaluate : 0.209 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 40 average time/residue: 0.0638 time to fit residues: 3.4855 Evaluate side-chains 40 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0278 time to fit residues: 0.7748 ------------------------------------------------------------------------------- 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: 10.0000 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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** ** 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: 0.7275 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 1830 Z= 0.313 Angle : 0.793 7.214 2490 Z= 0.420 Chirality : 0.051 0.168 290 Planarity : 0.002 0.010 330 Dihedral : 10.472 42.588 250 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.42), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.32), residues: 220 *********************** 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 36 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.199 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.0608 time to fit residues: 2.9052 Evaluate side-chains 31 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0226 time to fit residues: 0.3389 ------------------------------------------------------------------------------- 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: 20.0000 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** 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: 0.7221 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 1830 Z= 0.233 Angle : 0.705 7.135 2490 Z= 0.370 Chirality : 0.048 0.156 290 Planarity : 0.002 0.009 330 Dihedral : 9.678 41.334 250 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer Outliers : 3.33 % 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: -4.83 (0.42), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.32), residues: 220 *********************** 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 37 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.200 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.0650 time to fit residues: 3.0457 Evaluate side-chains 35 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0233 time to fit residues: 0.4461 ------------------------------------------------------------------------------- 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: 20.0000 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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** ** B 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: 0.7377 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.038 1830 Z= 0.470 Angle : 0.953 7.194 2490 Z= 0.512 Chirality : 0.058 0.182 290 Planarity : 0.003 0.015 330 Dihedral : 11.559 44.745 250 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer Outliers : 4.76 % 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: -4.89 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.32), residues: 220 *********************** 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 43 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.207 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 38 average time/residue: 0.0608 time to fit residues: 3.1962 Evaluate side-chains 36 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.220 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0246 time to fit residues: 0.5206 ------------------------------------------------------------------------------- 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: 0.0570 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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** ** 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: 0.7172 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 1830 Z= 0.179 Angle : 0.678 6.770 2490 Z= 0.348 Chirality : 0.046 0.146 290 Planarity : 0.002 0.009 330 Dihedral : 9.134 37.773 250 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer Outliers : 0.48 % 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: -4.82 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.33), residues: 220 ********************** 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 34 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.213 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0645 time to fit residues: 2.9959 Evaluate side-chains 34 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0230 time to fit residues: 0.3035 ------------------------------------------------------------------------------- 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: 20.0000 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.134904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.115995 restraints weight = 2796.390| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.39 r_work: 0.4108 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.4099 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work: 0.4089 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work: 0.4079 rms_B_bonded: 3.28 restraints_weight: 0.0625 r_work: 0.4069 rms_B_bonded: 3.37 restraints_weight: 0.0312 r_work: 0.4058 rms_B_bonded: 3.48 restraints_weight: 0.0156 r_work: 0.4047 rms_B_bonded: 3.60 restraints_weight: 0.0078 r_work: 0.4035 rms_B_bonded: 3.74 restraints_weight: 0.0039 r_work: 0.4024 rms_B_bonded: 3.89 restraints_weight: 0.0020 r_work: 0.4011 rms_B_bonded: 4.06 restraints_weight: 0.0010 r_work: 0.3999 rms_B_bonded: 4.25 restraints_weight: 0.0005 r_work: 0.3986 rms_B_bonded: 4.45 restraints_weight: 0.0002 r_work: 0.3972 rms_B_bonded: 4.66 restraints_weight: 0.0001 r_work: 0.3958 rms_B_bonded: 4.90 restraints_weight: 0.0001 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 1830 Z= 0.356 Angle : 0.844 6.891 2490 Z= 0.446 Chirality : 0.054 0.169 290 Planarity : 0.003 0.013 330 Dihedral : 10.787 42.964 250 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.55 % Favored : 80.45 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.33), residues: 220 =============================================================================== Job complete usr+sys time: 713.92 seconds wall clock time: 13 minutes 23.80 seconds (803.80 seconds total)