Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:33:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/11_2022/7uaq_26430.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/11_2022/7uaq_26430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/11_2022/7uaq_26430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/11_2022/7uaq_26430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/11_2022/7uaq_26430.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/11_2022/7uaq_26430.pdb" } resolution = 3.1 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= -0.003 sd= 0.035 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 Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.96, per 1000 atoms: 0.68 Number of scatterers: 4362 At special positions: 0 Unit cell: (96.82, 64.89, 89.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 850 8.00 N 723 7.00 C 2773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " " NAG C 1 " - " ASN A 149 " " NAG D 1 " - " ASN A 234 " " NAG L 301 " - " ASN L 20 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 669.8 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 4.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 removed outlier: 3.625A pdb=" N ASN L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.319A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.301A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.693A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.162A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.612A pdb=" N ALA H 88 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.936A pdb=" N ILE H 112 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.524A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 44 through 50 removed outlier: 6.653A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 231 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: 1.09 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1293 1.34 - 1.46: 1224 1.46 - 1.59: 1933 1.59 - 1.72: 0 1.72 - 1.84: 22 Bond restraints: 4472 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" N ILE A 197 " pdb=" CA ILE A 197 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 8.87e+00 bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N GLY L 101 " pdb=" CA GLY L 101 " ideal model delta sigma weight residual 1.447 1.474 -0.027 1.09e-02 8.42e+03 6.11e+00 bond pdb=" N VAL L 97 " pdb=" CA VAL L 97 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.07e+00 ... (remaining 4467 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.62: 60 104.62 - 112.02: 2068 112.02 - 119.41: 1578 119.41 - 126.81: 2310 126.81 - 134.21: 57 Bond angle restraints: 6073 Sorted by residual: angle pdb=" C ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.42 122.89 -12.47 1.99e+00 2.53e-01 3.93e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta sigma weight residual 110.45 101.66 8.79 1.44e+00 4.82e-01 3.73e+01 angle pdb=" CA GLY L 101 " pdb=" C GLY L 101 " pdb=" O GLY L 101 " ideal model delta sigma weight residual 122.29 117.98 4.31 8.10e-01 1.52e+00 2.83e+01 angle pdb=" N ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.49 101.68 8.81 1.69e+00 3.50e-01 2.72e+01 angle pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 123.12 128.85 -5.73 1.28e+00 6.08e-01 2.00e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 2309 14.78 - 29.56: 213 29.56 - 44.34: 47 44.34 - 59.13: 16 59.13 - 73.91: 4 Dihedral angle restraints: 2589 sinusoidal: 1047 harmonic: 1542 Sorted by residual: dihedral pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta harmonic sigma weight residual 122.80 110.48 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" CA GLN H 81 " pdb=" C GLN H 81 " pdb=" N MET H 82 " pdb=" CA MET H 82 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS L 54B" pdb=" C HIS L 54B" pdb=" N THR L 54C" pdb=" CA THR L 54C" ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 2586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 533 0.074 - 0.148: 129 0.148 - 0.222: 18 0.222 - 0.296: 3 0.296 - 0.370: 4 Chirality restraints: 687 Sorted by residual: chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.51 -2.14 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 684 not shown) Planarity restraints: 773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.010 2.00e-02 2.50e+03 7.50e-02 7.02e+01 pdb=" CG ASN A 165 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO A 225 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" CG ASN A 165 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.026 2.00e-02 2.50e+03 ... (remaining 770 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 4192 3.22 - 3.78: 6567 3.78 - 4.34: 9038 4.34 - 4.90: 14761 Nonbonded interactions: 34683 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR L 22 " pdb=" OE2 GLU L 70 " model vdw 2.102 2.440 nonbonded pdb=" OE2 GLU A 96 " pdb=" N ASN A 99 " model vdw 2.158 2.520 nonbonded pdb=" O SER H 30 " pdb=" OG1 THR H 52A" model vdw 2.174 2.440 nonbonded pdb=" OE1 GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.210 2.520 ... (remaining 34678 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 'B' selection = chain 'C' selection = chain 'D' } 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2773 2.51 5 N 723 2.21 5 O 850 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 9.530 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 0.054 4472 Z= 0.379 Angle : 1.163 12.470 6073 Z= 0.668 Chirality : 0.070 0.370 687 Planarity : 0.008 0.129 766 Dihedral : 12.641 73.906 1590 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.35), residues: 523 helix: -0.03 (1.56), residues: 11 sheet: -0.76 (0.46), residues: 139 loop : -2.30 (0.30), residues: 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1600 time to fit residues: 27.0218 Evaluate side-chains 86 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0457 time to fit residues: 0.6146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 4472 Z= 0.328 Angle : 0.826 10.322 6073 Z= 0.442 Chirality : 0.055 0.384 687 Planarity : 0.006 0.066 766 Dihedral : 5.862 26.064 642 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.34), residues: 523 helix: 1.13 (1.69), residues: 11 sheet: -0.62 (0.44), residues: 142 loop : -2.26 (0.29), residues: 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.1675 time to fit residues: 21.4948 Evaluate side-chains 97 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0476 time to fit residues: 1.3522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 4472 Z= 0.234 Angle : 0.718 7.387 6073 Z= 0.382 Chirality : 0.052 0.353 687 Planarity : 0.005 0.051 766 Dihedral : 5.615 22.437 642 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.35), residues: 523 helix: 1.76 (1.90), residues: 11 sheet: -0.24 (0.46), residues: 135 loop : -2.06 (0.30), residues: 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.1649 time to fit residues: 20.9201 Evaluate side-chains 98 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0519 time to fit residues: 1.5973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4472 Z= 0.228 Angle : 0.700 7.559 6073 Z= 0.371 Chirality : 0.051 0.330 687 Planarity : 0.005 0.048 766 Dihedral : 5.456 22.046 642 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.35), residues: 523 helix: -0.28 (1.55), residues: 17 sheet: -0.37 (0.43), residues: 147 loop : -2.10 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.1644 time to fit residues: 20.3898 Evaluate side-chains 95 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0451 time to fit residues: 1.0244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4472 Z= 0.250 Angle : 0.697 8.134 6073 Z= 0.369 Chirality : 0.051 0.320 687 Planarity : 0.005 0.047 766 Dihedral : 5.339 22.097 642 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.35), residues: 523 helix: -0.02 (1.61), residues: 17 sheet: -0.46 (0.43), residues: 147 loop : -2.06 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 0.1676 time to fit residues: 20.5392 Evaluate side-chains 92 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0465 time to fit residues: 1.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4472 Z= 0.245 Angle : 0.694 7.776 6073 Z= 0.370 Chirality : 0.050 0.316 687 Planarity : 0.005 0.046 766 Dihedral : 5.307 22.808 642 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.35), residues: 523 helix: -0.64 (1.47), residues: 17 sheet: -0.55 (0.43), residues: 142 loop : -2.00 (0.30), residues: 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.1630 time to fit residues: 18.6384 Evaluate side-chains 90 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0454 time to fit residues: 1.0943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 4472 Z= 0.336 Angle : 0.736 8.011 6073 Z= 0.395 Chirality : 0.050 0.325 687 Planarity : 0.005 0.047 766 Dihedral : 5.550 21.617 642 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.90 % Favored : 88.91 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.35), residues: 523 helix: -0.43 (1.58), residues: 17 sheet: -0.55 (0.44), residues: 140 loop : -2.07 (0.30), residues: 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.488 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.1754 time to fit residues: 21.0266 Evaluate side-chains 94 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0593 time to fit residues: 1.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4472 Z= 0.221 Angle : 0.746 10.182 6073 Z= 0.392 Chirality : 0.050 0.314 687 Planarity : 0.005 0.048 766 Dihedral : 5.375 22.043 642 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.35), residues: 523 helix: -0.58 (1.48), residues: 17 sheet: -0.71 (0.42), residues: 150 loop : -2.04 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.1601 time to fit residues: 19.4957 Evaluate side-chains 91 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0436 time to fit residues: 0.9401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 0.0670 chunk 49 optimal weight: 0.0010 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4472 Z= 0.217 Angle : 0.723 10.413 6073 Z= 0.379 Chirality : 0.049 0.316 687 Planarity : 0.005 0.047 766 Dihedral : 5.252 21.468 642 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.35), residues: 523 helix: -0.52 (1.50), residues: 17 sheet: -0.74 (0.42), residues: 150 loop : -1.96 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.1740 time to fit residues: 20.5633 Evaluate side-chains 87 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0424 time to fit residues: 0.8239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4472 Z= 0.236 Angle : 0.743 10.504 6073 Z= 0.394 Chirality : 0.048 0.275 687 Planarity : 0.005 0.048 766 Dihedral : 5.300 20.422 642 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.36), residues: 523 helix: -0.59 (1.48), residues: 17 sheet: -0.80 (0.42), residues: 150 loop : -1.92 (0.32), residues: 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.1756 time to fit residues: 19.6415 Evaluate side-chains 86 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0472 time to fit residues: 0.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** 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 = 0.3911 r_free = 0.3911 target = 0.111153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086914 restraints weight = 10737.912| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 5.00 r_work: 0.3481 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work: 0.3461 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work: 0.3451 rms_B_bonded: 4.74 restraints_weight: 0.0625 r_work: 0.3441 rms_B_bonded: 4.79 restraints_weight: 0.0312 r_work: 0.3431 rms_B_bonded: 4.87 restraints_weight: 0.0156 r_work: 0.3421 rms_B_bonded: 4.95 restraints_weight: 0.0078 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4472 Z= 0.293 Angle : 0.753 9.869 6073 Z= 0.398 Chirality : 0.049 0.328 687 Planarity : 0.005 0.048 766 Dihedral : 5.443 19.026 642 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.36), residues: 523 helix: 2.42 (1.96), residues: 11 sheet: -0.92 (0.43), residues: 150 loop : -1.91 (0.31), residues: 362 =============================================================================== Job complete usr+sys time: 1439.92 seconds wall clock time: 26 minutes 52.22 seconds (1612.22 seconds total)