Starting phenix.real_space_refine (version: dev) on Sun Dec 11 15:47:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2022/7p2p_13171_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2022/7p2p_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_2022/7p2p_13171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2022/7p2p_13171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2022/7p2p_13171_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/12_2022/7p2p_13171_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Convert atoms to be neutral 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 3 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.29, per 1000 atoms: 0.69 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: 2.30 Conformation dependent library (CDL) restraints added in 723.9 milliseconds 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: 0.23 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: 1.13 Time building geometry restraints manager: 2.35 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=" 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 bond pdb=" N ARG D 138 " pdb=" CA ARG D 138 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.37e+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: 2638 14.13 - 28.27: 194 28.27 - 42.40: 73 42.40 - 56.54: 4 56.54 - 70.67: 2 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: 712 0.122 - 0.244: 43 0.244 - 0.366: 1 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=" 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 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.43e+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 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. 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: 0.300 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: 2.060 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 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 0.051 4900 Z= 0.294 Angle : 1.076 10.353 6634 Z= 0.561 Chirality : 0.066 0.610 757 Planarity : 0.007 0.046 820 Dihedral : 11.208 70.669 1811 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 0.19 % 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 *********************** 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 : 0.606 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: 0.2317 time to fit residues: 53.7240 Evaluate side-chains 103 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0438 time to fit residues: 0.7955 ------------------------------------------------------------------------------- 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: 0.6739 moved from start: 0.3895 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= 0.183 Angle : 0.717 7.957 6634 Z= 0.367 Chirality : 0.050 0.524 757 Planarity : 0.005 0.052 820 Dihedral : 5.326 33.497 675 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.19 % 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 *********************** 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 : 0.605 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: 1 outliers final: 1 residues processed: 143 average time/residue: 0.1979 time to fit residues: 34.7127 Evaluate side-chains 107 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0714 time to fit residues: 0.8970 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 B 84 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4900 Z= 0.270 Angle : 0.797 10.730 6634 Z= 0.404 Chirality : 0.050 0.445 757 Planarity : 0.005 0.038 820 Dihedral : 5.501 30.792 675 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.32), residues: 579 helix: 0.10 (0.34), residues: 219 sheet: -0.47 (0.69), residues: 59 loop : -3.44 (0.30), residues: 301 *********************** 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 129 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.621 Fit side-chains 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: 129 average time/residue: 0.1961 time to fit residues: 31.0370 Evaluate side-chains 91 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7932 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 128 GLN B 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5293 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= 0.222 Angle : 0.727 8.240 6634 Z= 0.372 Chirality : 0.049 0.430 757 Planarity : 0.004 0.029 820 Dihedral : 5.420 32.550 675 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.33), residues: 579 helix: 0.24 (0.34), residues: 219 sheet: -0.64 (0.63), residues: 69 loop : -3.37 (0.31), residues: 291 *********************** 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 130 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.618 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: 130 average time/residue: 0.1735 time to fit residues: 28.4151 Evaluate side-chains 104 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8658 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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: 0.7032 moved from start: 0.5821 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= 0.215 Angle : 0.723 9.172 6634 Z= 0.368 Chirality : 0.048 0.412 757 Planarity : 0.004 0.028 820 Dihedral : 5.401 32.477 675 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.33), residues: 579 helix: 0.35 (0.34), residues: 218 sheet: -0.47 (0.69), residues: 61 loop : -3.31 (0.31), residues: 300 *********************** 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 126 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1750 time to fit residues: 27.7107 Evaluate side-chains 98 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8147 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7092 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4900 Z= 0.246 Angle : 0.752 7.613 6634 Z= 0.387 Chirality : 0.048 0.404 757 Planarity : 0.004 0.027 820 Dihedral : 5.452 31.678 675 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.33), residues: 579 helix: 0.35 (0.34), residues: 216 sheet: -0.67 (0.64), residues: 69 loop : -3.34 (0.31), residues: 294 *********************** 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 117 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1670 time to fit residues: 24.8608 Evaluate side-chains 97 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7902 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.7122 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4900 Z= 0.265 Angle : 0.775 9.736 6634 Z= 0.397 Chirality : 0.049 0.397 757 Planarity : 0.005 0.049 820 Dihedral : 5.531 31.380 675 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.33), residues: 579 helix: 0.27 (0.34), residues: 216 sheet: -0.94 (0.63), residues: 70 loop : -3.34 (0.31), residues: 293 *********************** 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 114 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.618 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: 114 average time/residue: 0.1810 time to fit residues: 25.8874 Evaluate side-chains 90 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8938 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 21 optimal weight: 0.0270 chunk 39 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 overall best weight: 1.0056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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: 0.7056 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4900 Z= 0.187 Angle : 0.755 8.109 6634 Z= 0.382 Chirality : 0.049 0.397 757 Planarity : 0.004 0.045 820 Dihedral : 5.353 33.692 675 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.19 % 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: -2.12 (0.34), residues: 579 helix: 0.52 (0.35), residues: 216 sheet: -0.63 (0.64), residues: 69 loop : -3.29 (0.32), residues: 294 *********************** 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 118 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.632 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: 118 average time/residue: 0.1914 time to fit residues: 28.0050 Evaluate side-chains 90 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8383 ------------------------------------------------------------------------------- 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: 0.0970 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 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: 0.7030 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4900 Z= 0.181 Angle : 0.764 11.029 6634 Z= 0.384 Chirality : 0.048 0.397 757 Planarity : 0.004 0.044 820 Dihedral : 5.322 33.800 675 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.19 % 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: -2.01 (0.34), residues: 579 helix: 0.58 (0.35), residues: 216 sheet: -0.45 (0.64), residues: 69 loop : -3.24 (0.32), residues: 294 *********************** 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 116 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.613 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: 116 average time/residue: 0.1829 time to fit residues: 26.6515 Evaluate side-chains 90 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8399 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.4760 ------------------------------------------------------------------------------- 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 ** 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: 0.6998 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4900 Z= 0.169 Angle : 0.743 8.334 6634 Z= 0.375 Chirality : 0.048 0.398 757 Planarity : 0.005 0.048 820 Dihedral : 5.298 34.646 675 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 0.19 % 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: -1.96 (0.34), residues: 579 helix: 0.65 (0.35), residues: 216 sheet: -0.76 (0.59), residues: 80 loop : -3.22 (0.33), residues: 283 ********************** 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 : 0.562 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: 0.1805 time to fit residues: 27.4835 Evaluate side-chains 101 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7101 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** 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 = 0.3551 r_free = 0.3551 target = 0.078839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064371 restraints weight = 29200.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065994 restraints weight = 22172.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067261 restraints weight = 17819.788| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6847 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= 0.180 Angle : 0.766 10.530 6634 Z= 0.385 Chirality : 0.048 0.399 757 Planarity : 0.005 0.063 820 Dihedral : 5.248 33.860 675 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.19 % 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: -1.97 (0.34), residues: 579 helix: 0.62 (0.35), residues: 216 sheet: -0.67 (0.60), residues: 80 loop : -3.22 (0.33), residues: 283 =============================================================================== Job complete usr+sys time: 1299.56 seconds wall clock time: 24 minutes 11.91 seconds (1451.91 seconds total)