Starting phenix.real_space_refine on Thu Dec 7 21:16:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2023/7p2p_13171_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2023/7p2p_13171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2023/7p2p_13171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2023/7p2p_13171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2023/7p2p_13171_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2023/7p2p_13171_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3109 2.51 5 N 785 2.21 5 O 866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4783 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1189 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.11, per 1000 atoms: 0.65 Number of scatterers: 4783 At special positions: 0 Unit cell: (79.38, 84.24, 131.22, 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 23 16.00 O 866 8.00 N 785 7.00 C 3109 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 38.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 15 through 43 Processing helix chain 'A' and resid 148 through 158 removed outlier: 4.210A pdb=" N VAL A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 Processing helix chain 'C' and resid 53 through 72 Processing helix chain 'C' and resid 79 through 104 Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.894A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 removed outlier: 3.559A pdb=" N ALA C 207 " --> pdb=" O VAL C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 208 through 224 removed outlier: 4.018A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 110 Processing helix chain 'D' and resid 111 through 131 removed outlier: 4.352A pdb=" N THR D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 141 through 144 removed outlier: 4.021A pdb=" N TRP D 144 " --> pdb=" O PRO D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.151A pdb=" N ILE A 101 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 102 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.535A pdb=" N PHE A 111 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.078A pdb=" N LEU B 48 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR B 67 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASN B 50 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 65 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 64 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 90 removed outlier: 4.321A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 151 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 88 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 147 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B 146 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B 164 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TRP B 148 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 162 " --> pdb=" O TRP B 148 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 150 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL B 160 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77 removed outlier: 4.313A pdb=" N VAL C 142 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 621 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: 1.20 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 816 1.33 - 1.45: 1298 1.45 - 1.57: 2744 1.57 - 1.69: 1 1.69 - 1.81: 41 Bond restraints: 4900 Sorted by residual: bond pdb=" N LEU D 131 " pdb=" CA LEU D 131 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.86e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" N LEU A 69 " pdb=" CA LEU A 69 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N ILE D 136 " pdb=" CA ILE D 136 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" C PRO D 135 " pdb=" O PRO D 135 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.26e-02 6.30e+03 6.63e+00 ... (remaining 4895 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.76: 156 106.76 - 113.64: 2624 113.64 - 120.52: 2007 120.52 - 127.40: 1798 127.40 - 134.28: 49 Bond angle restraints: 6634 Sorted by residual: angle pdb=" N PRO D 141 " pdb=" CA PRO D 141 " pdb=" C PRO D 141 " ideal model delta sigma weight residual 113.57 106.87 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.13 -9.59 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C LYS B 49 " pdb=" N ASN B 50 " pdb=" CA ASN B 50 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C CYS B 26 " pdb=" N PHE B 27 " pdb=" CA PHE B 27 " ideal model delta sigma weight residual 121.66 113.71 7.95 1.76e+00 3.23e-01 2.04e+01 ... (remaining 6629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 2635 14.13 - 28.27: 194 28.27 - 42.40: 72 42.40 - 56.54: 6 56.54 - 70.67: 4 Dihedral angle restraints: 2911 sinusoidal: 1205 harmonic: 1706 Sorted by residual: dihedral pdb=" CA LYS C 111 " pdb=" C LYS C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LEU D 75 " pdb=" C LEU D 75 " pdb=" N PRO D 76 " pdb=" CA PRO D 76 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO D 133 " pdb=" C PRO D 133 " pdb=" N TRP D 134 " pdb=" CA TRP D 134 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 707 0.122 - 0.244: 47 0.244 - 0.366: 2 0.366 - 0.488: 0 0.488 - 0.610: 1 Chirality restraints: 757 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE A 68 " pdb=" N PHE A 68 " pdb=" C PHE A 68 " pdb=" CB PHE A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 754 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 22 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C VAL A 22 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 22 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 23 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 216 " 0.013 2.00e-02 2.50e+03 1.71e-02 4.37e+00 pdb=" CG HIS C 216 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS C 216 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS C 216 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS C 216 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 216 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 24 " 0.012 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE B 24 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 24 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 24 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 24 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 24 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 24 " -0.000 2.00e-02 2.50e+03 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1464 2.84 - 3.35: 4304 3.35 - 3.87: 7635 3.87 - 4.38: 7919 4.38 - 4.90: 13585 Nonbonded interactions: 34907 Sorted by model distance: nonbonded pdb=" O THR A 43 " pdb=" ND2 ASN A 71 " model vdw 2.325 2.520 nonbonded pdb=" O ILE A 87 " pdb=" N GLU A 91 " model vdw 2.343 2.520 nonbonded pdb=" O SER D 126 " pdb=" OG1 THR D 130 " model vdw 2.349 2.440 nonbonded pdb=" O TRP C 51 " pdb=" OG1 THR D 77 " model vdw 2.351 2.440 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.353 2.440 ... (remaining 34902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.350 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: 0.000 Extract box with map and model: 1.870 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.005 0.054 4900 Z= 0.315 Angle : 1.104 10.353 6634 Z= 0.564 Chirality : 0.067 0.610 757 Planarity : 0.007 0.046 820 Dihedral : 11.497 70.669 1811 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.19 % Allowed : 8.06 % Favored : 91.75 % 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: -3.94 (0.28), residues: 579 helix: -1.72 (0.27), residues: 208 sheet: -1.10 (0.63), residues: 57 loop : -3.72 (0.28), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 80 HIS 0.021 0.002 HIS C 216 PHE 0.036 0.004 PHE B 24 TYR 0.018 0.002 TYR B 174 ARG 0.005 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.2380 time to fit residues: 54.9956 Evaluate side-chains 103 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0486 time to fit residues: 0.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 128 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4900 Z= 0.177 Angle : 0.725 8.002 6634 Z= 0.367 Chirality : 0.049 0.433 757 Planarity : 0.005 0.051 820 Dihedral : 6.742 57.320 675 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.19 % Allowed : 5.57 % Favored : 94.24 % 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: -2.73 (0.32), residues: 579 helix: -0.06 (0.34), residues: 211 sheet: -1.12 (0.64), residues: 65 loop : -3.45 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.015 0.001 HIS C 216 PHE 0.026 0.002 PHE C 94 TYR 0.020 0.002 TYR D 117 ARG 0.005 0.001 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.569 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: 1 outliers final: 1 residues processed: 143 average time/residue: 0.2075 time to fit residues: 36.0095 Evaluate side-chains 106 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0883 time to fit residues: 0.9227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4900 Z= 0.173 Angle : 0.714 8.709 6634 Z= 0.357 Chirality : 0.048 0.387 757 Planarity : 0.004 0.037 820 Dihedral : 6.574 55.834 675 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.34), residues: 579 helix: 0.45 (0.36), residues: 213 sheet: -0.86 (0.65), residues: 65 loop : -3.23 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 148 HIS 0.015 0.001 HIS C 216 PHE 0.030 0.002 PHE B 12 TYR 0.027 0.001 TYR D 117 ARG 0.006 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.597 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: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1879 time to fit residues: 30.5371 Evaluate side-chains 97 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 76 ASN B 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4900 Z= 0.182 Angle : 0.699 7.135 6634 Z= 0.355 Chirality : 0.047 0.363 757 Planarity : 0.004 0.031 820 Dihedral : 6.402 55.597 675 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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: -2.02 (0.34), residues: 579 helix: 0.64 (0.36), residues: 213 sheet: -0.69 (0.67), residues: 65 loop : -3.16 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 51 HIS 0.014 0.001 HIS C 216 PHE 0.028 0.002 PHE D 112 TYR 0.028 0.002 TYR D 117 ARG 0.007 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.516 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: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1717 time to fit residues: 27.0078 Evaluate side-chains 97 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 48 optimal weight: 0.2980 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4900 Z= 0.153 Angle : 0.702 8.332 6634 Z= 0.346 Chirality : 0.047 0.361 757 Planarity : 0.004 0.030 820 Dihedral : 6.152 55.599 675 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.35), residues: 579 helix: 0.89 (0.37), residues: 213 sheet: -0.95 (0.62), residues: 72 loop : -3.09 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.014 0.001 HIS C 216 PHE 0.038 0.002 PHE B 12 TYR 0.025 0.001 TYR D 117 ARG 0.007 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.504 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: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1734 time to fit residues: 26.9652 Evaluate side-chains 97 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4900 Z= 0.171 Angle : 0.694 6.990 6634 Z= 0.347 Chirality : 0.047 0.348 757 Planarity : 0.004 0.027 820 Dihedral : 6.002 54.918 675 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.35), residues: 579 helix: 0.88 (0.36), residues: 218 sheet: -0.85 (0.62), residues: 72 loop : -3.10 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 51 HIS 0.015 0.001 HIS C 216 PHE 0.017 0.002 PHE D 112 TYR 0.027 0.001 TYR D 117 ARG 0.008 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.609 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: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1860 time to fit residues: 29.7297 Evaluate side-chains 101 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4900 Z= 0.163 Angle : 0.715 9.013 6634 Z= 0.356 Chirality : 0.047 0.350 757 Planarity : 0.004 0.026 820 Dihedral : 5.899 54.989 675 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.35), residues: 579 helix: 0.96 (0.36), residues: 217 sheet: -0.70 (0.63), residues: 72 loop : -3.07 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 144 HIS 0.015 0.001 HIS C 216 PHE 0.034 0.002 PHE B 12 TYR 0.022 0.001 TYR D 117 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.697 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: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1917 time to fit residues: 32.2750 Evaluate side-chains 98 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4900 Z= 0.199 Angle : 0.743 8.914 6634 Z= 0.372 Chirality : 0.047 0.334 757 Planarity : 0.004 0.024 820 Dihedral : 6.015 53.861 675 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.19 % Allowed : 1.73 % Favored : 98.08 % 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: -1.82 (0.35), residues: 579 helix: 0.78 (0.36), residues: 217 sheet: -0.50 (0.65), residues: 72 loop : -3.16 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 144 HIS 0.013 0.001 HIS C 216 PHE 0.022 0.002 PHE D 112 TYR 0.028 0.002 TYR D 117 ARG 0.006 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1662 time to fit residues: 25.6965 Evaluate side-chains 101 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4900 Z= 0.165 Angle : 0.736 9.306 6634 Z= 0.364 Chirality : 0.047 0.341 757 Planarity : 0.004 0.055 820 Dihedral : 5.854 54.448 675 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.35), residues: 579 helix: 0.98 (0.36), residues: 217 sheet: -0.38 (0.66), residues: 72 loop : -3.04 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 144 HIS 0.017 0.001 HIS C 216 PHE 0.017 0.002 PHE C 94 TYR 0.023 0.001 TYR D 117 ARG 0.003 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1723 time to fit residues: 28.7830 Evaluate side-chains 98 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 0.0670 chunk 40 optimal weight: 0.0010 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 1.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4900 Z= 0.187 Angle : 0.756 9.199 6634 Z= 0.379 Chirality : 0.047 0.341 757 Planarity : 0.005 0.049 820 Dihedral : 5.897 53.560 675 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % 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: -1.70 (0.35), residues: 579 helix: 0.92 (0.36), residues: 219 sheet: -0.34 (0.66), residues: 72 loop : -3.18 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 144 HIS 0.017 0.001 HIS C 216 PHE 0.019 0.002 PHE C 94 TYR 0.032 0.002 TYR C 121 ARG 0.008 0.001 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1733 time to fit residues: 26.6098 Evaluate side-chains 98 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0070 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.080974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065955 restraints weight = 28291.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067526 restraints weight = 21956.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068812 restraints weight = 17941.821| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4900 Z= 0.164 Angle : 0.742 9.476 6634 Z= 0.368 Chirality : 0.047 0.340 757 Planarity : 0.005 0.053 820 Dihedral : 5.887 53.746 675 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.35), residues: 579 helix: 0.86 (0.36), residues: 219 sheet: -0.40 (0.61), residues: 80 loop : -3.22 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 144 HIS 0.016 0.001 HIS C 216 PHE 0.020 0.002 PHE C 94 TYR 0.024 0.001 TYR C 121 ARG 0.004 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.16 seconds wall clock time: 25 minutes 0.55 seconds (1500.55 seconds total)