Starting phenix.real_space_refine on Wed Nov 15 08:01:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/11_2023/7n8n_24238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/11_2023/7n8n_24238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/11_2023/7n8n_24238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/11_2023/7n8n_24238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/11_2023/7n8n_24238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/11_2023/7n8n_24238.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 30 5.16 5 C 6180 2.51 5 N 2053 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2543 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2576 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Time building chain proxies: 6.08, per 1000 atoms: 0.55 Number of scatterers: 11121 At special positions: 0 Unit cell: (86.265, 111.825, 116.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 248 15.00 O 2610 8.00 N 2053 7.00 C 6180 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: 7.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 67.4% alpha, 0.5% beta 124 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.561A pdb=" N VAL A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.975A pdb=" N GLN A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 172 through 201 Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 56 through 81 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 4.885A pdb=" N GLU B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.562A pdb=" N VAL C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.976A pdb=" N GLN C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 172 through 201 Processing helix chain 'C' and resid 207 through 219 Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 56 through 81 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 127 Processing helix chain 'D' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 removed outlier: 4.884A pdb=" N GLU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 205 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85 388 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2475 1.33 - 1.45: 3579 1.45 - 1.57: 5210 1.57 - 1.69: 496 1.69 - 1.81: 52 Bond restraints: 11812 Sorted by residual: bond pdb=" CZ ARG B 157 " pdb=" NH2 ARG B 157 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.01e+00 bond pdb=" CZ ARG D 157 " pdb=" NH2 ARG D 157 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" CA VAL A 56 " pdb=" CB VAL A 56 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.77e+00 bond pdb=" CA VAL C 56 " pdb=" CB VAL C 56 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.30e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 11807 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.25: 931 104.25 - 111.35: 6057 111.35 - 118.45: 3564 118.45 - 125.55: 5631 125.55 - 132.65: 814 Bond angle restraints: 16997 Sorted by residual: angle pdb=" CB MET C 157 " pdb=" CG MET C 157 " pdb=" SD MET C 157 " ideal model delta sigma weight residual 112.70 102.55 10.15 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " ideal model delta sigma weight residual 112.70 102.57 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CA LEU B 166 " pdb=" CB LEU B 166 " pdb=" CG LEU B 166 " ideal model delta sigma weight residual 116.30 105.03 11.27 3.50e+00 8.16e-02 1.04e+01 angle pdb=" CA LEU D 166 " pdb=" CB LEU D 166 " pdb=" CG LEU D 166 " ideal model delta sigma weight residual 116.30 105.03 11.27 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C4 DT I -64 " pdb=" C5 DT I -64 " pdb=" C7 DT I -64 " ideal model delta sigma weight residual 122.40 117.59 4.81 1.50e+00 4.44e-01 1.03e+01 ... (remaining 16992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5048 34.91 - 69.81: 1196 69.81 - 104.72: 17 104.72 - 139.63: 2 139.63 - 174.54: 3 Dihedral angle restraints: 6266 sinusoidal: 3996 harmonic: 2270 Sorted by residual: dihedral pdb=" CA SER C 131 " pdb=" C SER C 131 " pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta harmonic sigma weight residual -180.00 -63.39 -116.61 0 5.00e+00 4.00e-02 5.44e+02 dihedral pdb=" CA SER A 131 " pdb=" C SER A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual -180.00 -63.45 -116.55 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CA LYS C 112 " pdb=" C LYS C 112 " pdb=" N GLY C 113 " pdb=" CA GLY C 113 " ideal model delta harmonic sigma weight residual -180.00 -99.23 -80.77 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 6263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1311 0.036 - 0.072: 474 0.072 - 0.108: 133 0.108 - 0.143: 39 0.143 - 0.179: 7 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CG LEU C 41 " pdb=" CB LEU C 41 " pdb=" CD1 LEU C 41 " pdb=" CD2 LEU C 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1961 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 135 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C LYS B 135 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS B 135 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 136 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 135 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C LYS D 135 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS D 135 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 136 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 65 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" CG ASN D 65 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN D 65 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN D 65 " -0.016 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 246 2.61 - 3.18: 10949 3.18 - 3.75: 22515 3.75 - 4.33: 27845 4.33 - 4.90: 37785 Nonbonded interactions: 99340 Sorted by model distance: nonbonded pdb=" O GLU A 132 " pdb=" OG SER A 135 " model vdw 2.035 2.440 nonbonded pdb=" O GLU C 132 " pdb=" OG SER C 135 " model vdw 2.036 2.440 nonbonded pdb=" OG SER A 185 " pdb=" O GLY D 219 " model vdw 2.101 2.440 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 38 " model vdw 2.103 2.440 nonbonded pdb=" O LYS C 35 " pdb=" OG1 THR C 38 " model vdw 2.104 2.440 ... (remaining 99335 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 3.980 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 37.490 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 0.045 11812 Z= 0.360 Angle : 0.849 11.271 16997 Z= 0.504 Chirality : 0.042 0.179 1964 Planarity : 0.006 0.054 1276 Dihedral : 28.108 174.537 4798 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.28), residues: 790 helix: -0.13 (0.22), residues: 484 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2346 time to fit residues: 60.8384 Evaluate side-chains 110 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11812 Z= 0.289 Angle : 0.748 10.713 16997 Z= 0.429 Chirality : 0.041 0.258 1964 Planarity : 0.006 0.065 1276 Dihedral : 31.566 174.430 3342 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 4.95 % Allowed : 12.07 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.28), residues: 790 helix: 0.09 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.67 (0.32), residues: 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 147 average time/residue: 0.2146 time to fit residues: 46.1064 Evaluate side-chains 132 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1061 time to fit residues: 5.0068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 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 32 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 56 GLN B 65 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN D 65 ASN D 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 11812 Z= 0.400 Angle : 0.776 6.789 16997 Z= 0.452 Chirality : 0.042 0.177 1964 Planarity : 0.007 0.076 1276 Dihedral : 31.700 176.964 3342 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 30.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.75 % Favored : 90.00 % Rotamer: Outliers : 3.41 % Allowed : 16.41 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.28), residues: 790 helix: 0.00 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.83 (0.31), residues: 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 130 average time/residue: 0.2086 time to fit residues: 40.0709 Evaluate side-chains 110 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1070 time to fit residues: 2.9884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 40.0000 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 167 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11812 Z= 0.273 Angle : 0.718 7.268 16997 Z= 0.415 Chirality : 0.040 0.184 1964 Planarity : 0.006 0.075 1276 Dihedral : 31.744 178.204 3342 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.39 % Rotamer: Outliers : 1.86 % Allowed : 21.52 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.29), residues: 790 helix: 0.25 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.69 (0.32), residues: 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 0.1895 time to fit residues: 35.2813 Evaluate side-chains 108 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1058 time to fit residues: 2.1865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11812 Z= 0.283 Angle : 0.707 7.788 16997 Z= 0.409 Chirality : 0.039 0.224 1964 Planarity : 0.006 0.076 1276 Dihedral : 31.703 179.419 3342 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.72 % Favored : 92.03 % Rotamer: Outliers : 1.55 % Allowed : 24.15 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 790 helix: 0.33 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.68 (0.33), residues: 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.2264 time to fit residues: 37.6791 Evaluate side-chains 106 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1763 time to fit residues: 2.8885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11812 Z= 0.232 Angle : 0.692 8.388 16997 Z= 0.397 Chirality : 0.038 0.156 1964 Planarity : 0.005 0.074 1276 Dihedral : 31.686 179.898 3342 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Rotamer: Outliers : 1.55 % Allowed : 25.70 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.91 (0.29), residues: 790 helix: 0.42 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.51 (0.33), residues: 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 120 average time/residue: 0.2062 time to fit residues: 36.4065 Evaluate side-chains 108 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1005 time to fit residues: 1.4748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11812 Z= 0.209 Angle : 0.688 9.629 16997 Z= 0.390 Chirality : 0.038 0.185 1964 Planarity : 0.005 0.072 1276 Dihedral : 31.594 179.925 3342 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.58 % Favored : 93.16 % Rotamer: Outliers : 1.08 % Allowed : 28.02 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.71 (0.29), residues: 790 helix: 0.59 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.45 (0.33), residues: 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 119 average time/residue: 0.2276 time to fit residues: 39.3781 Evaluate side-chains 106 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1102 time to fit residues: 1.4494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11812 Z= 0.311 Angle : 0.716 9.515 16997 Z= 0.412 Chirality : 0.040 0.205 1964 Planarity : 0.006 0.074 1276 Dihedral : 31.747 178.563 3342 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.61 % Favored : 91.14 % Rotamer: Outliers : 1.08 % Allowed : 30.80 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.88 (0.29), residues: 790 helix: 0.43 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.52 (0.34), residues: 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.1962 time to fit residues: 31.2450 Evaluate side-chains 100 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1157 time to fit residues: 1.7254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11812 Z= 0.273 Angle : 0.713 9.756 16997 Z= 0.409 Chirality : 0.040 0.215 1964 Planarity : 0.006 0.073 1276 Dihedral : 31.819 176.953 3342 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.22 % Favored : 92.53 % Rotamer: Outliers : 0.93 % Allowed : 31.42 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.87 (0.29), residues: 790 helix: 0.44 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 104 average time/residue: 0.1954 time to fit residues: 30.7338 Evaluate side-chains 99 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 11812 Z= 0.383 Angle : 0.780 10.329 16997 Z= 0.451 Chirality : 0.043 0.203 1964 Planarity : 0.006 0.076 1276 Dihedral : 32.081 175.612 3342 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 31.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.25 % Favored : 89.49 % Rotamer: Outliers : 0.77 % Allowed : 32.04 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.28), residues: 790 helix: 0.03 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -2.76 (0.33), residues: 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 107 average time/residue: 0.1957 time to fit residues: 31.9870 Evaluate side-chains 107 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1164 time to fit residues: 2.1068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.059714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.043947 restraints weight = 70272.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045493 restraints weight = 42241.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.046558 restraints weight = 29979.423| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11812 Z= 0.247 Angle : 0.722 10.552 16997 Z= 0.411 Chirality : 0.040 0.249 1964 Planarity : 0.006 0.073 1276 Dihedral : 32.005 174.607 3342 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.47 % Favored : 92.28 % Rotamer: Outliers : 0.46 % Allowed : 32.97 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.29), residues: 790 helix: 0.37 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.68 (0.33), residues: 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1797.48 seconds wall clock time: 36 minutes 17.15 seconds (2177.15 seconds total)