Starting phenix.real_space_refine on Thu Dec 7 18:19:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/12_2023/8h9r_34578.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/12_2023/8h9r_34578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/12_2023/8h9r_34578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/12_2023/8h9r_34578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/12_2023/8h9r_34578.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/12_2023/8h9r_34578.pdb" } resolution = 3.97 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= 0.009 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 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 20": "OE1" <-> "OE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 142": "OE1" <-> "OE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 96": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 151": "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: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 2.20, per 1000 atoms: 0.65 Number of scatterers: 3381 At special positions: 0 Unit cell: (91.98, 94.9, 206.59, 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 11 16.00 O 634 8.00 N 560 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 613.3 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 74.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 32 through 48 removed outlier: 3.559A pdb=" N VAL K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.792A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 removed outlier: 3.782A pdb=" N VAL K 182 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.303A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.768A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 22 removed outlier: 5.643A pdb=" N ASN M 22 " --> pdb=" O ILE M 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 19 through 22' Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.753A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 Processing helix chain 'M' and resid 156 through 160 Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 239 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1089 1.34 - 1.46: 745 1.46 - 1.58: 1601 1.58 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N ASP L 97 " pdb=" CA ASP L 97 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 bond pdb=" N ARG L 48 " pdb=" CA ARG L 48 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.22e+00 bond pdb=" N ASN M 136 " pdb=" CA ASN M 136 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.67e+00 bond pdb=" CA LYS M 146 " pdb=" C LYS M 146 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.38e-02 5.25e+03 5.36e+00 bond pdb=" N THR M 131 " pdb=" CA THR M 131 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.34e-02 5.57e+03 5.17e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.02: 87 106.02 - 113.01: 1860 113.01 - 120.01: 1280 120.01 - 127.01: 1408 127.01 - 134.01: 39 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N MET L 81 " pdb=" CA MET L 81 " pdb=" C MET L 81 " ideal model delta sigma weight residual 113.55 104.90 8.65 1.26e+00 6.30e-01 4.71e+01 angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.31 115.19 5.12 1.52e+00 4.33e-01 1.13e+01 angle pdb=" CA THR M 131 " pdb=" C THR M 131 " pdb=" O THR M 131 " ideal model delta sigma weight residual 121.87 118.12 3.75 1.16e+00 7.43e-01 1.05e+01 angle pdb=" N LYS K 152 " pdb=" CA LYS K 152 " pdb=" C LYS K 152 " ideal model delta sigma weight residual 111.28 108.29 2.99 1.09e+00 8.42e-01 7.52e+00 angle pdb=" CA ARG L 48 " pdb=" C ARG L 48 " pdb=" O ARG L 48 " ideal model delta sigma weight residual 120.82 118.04 2.78 1.05e+00 9.07e-01 7.02e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1850 16.75 - 33.49: 202 33.49 - 50.24: 46 50.24 - 66.99: 10 66.99 - 83.73: 5 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PHE L 93 " pdb=" C PHE L 93 " pdb=" N LYS L 94 " pdb=" CA LYS L 94 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 350 0.045 - 0.090: 127 0.090 - 0.134: 28 0.134 - 0.179: 2 0.179 - 0.224: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA MET L 81 " pdb=" N MET L 81 " pdb=" C MET L 81 " pdb=" CB MET L 81 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE M 125 " pdb=" N ILE M 125 " pdb=" C ILE M 125 " pdb=" CB ILE M 125 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA LYS K 152 " pdb=" N LYS K 152 " pdb=" C LYS K 152 " pdb=" CB LYS K 152 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 96 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C GLU L 96 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU L 96 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP L 97 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 71 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ILE K 71 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE K 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS K 72 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 80 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C GLN L 80 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN L 80 " -0.011 2.00e-02 2.50e+03 pdb=" N MET L 81 " -0.009 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 782 2.78 - 3.31: 3734 3.31 - 3.84: 5690 3.84 - 4.37: 6055 4.37 - 4.90: 9558 Nonbonded interactions: 25819 Sorted by model distance: nonbonded pdb=" NE2 HIS K 158 " pdb=" O MET L 87 " model vdw 2.244 2.520 nonbonded pdb=" O ILE M 26 " pdb=" OG SER M 29 " model vdw 2.292 2.440 nonbonded pdb=" O LEU K 136 " pdb=" OG1 THR K 139 " model vdw 2.302 2.440 nonbonded pdb=" OE2 GLU K 111 " pdb=" NH2 ARG M 110 " model vdw 2.313 2.520 nonbonded pdb=" O VAL L 61 " pdb=" OG SER L 64 " model vdw 2.318 2.440 ... (remaining 25814 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: 6.640 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: 26.880 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3456 Z= 0.393 Angle : 0.793 8.648 4674 Z= 0.488 Chirality : 0.046 0.224 508 Planarity : 0.005 0.035 603 Dihedral : 15.254 83.733 1299 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.99 (0.36), residues: 413 helix: -0.76 (0.26), residues: 277 sheet: None (None), residues: 0 loop : -2.31 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 176 HIS 0.011 0.003 HIS K 172 PHE 0.021 0.003 PHE M 69 TYR 0.015 0.002 TYR K 145 ARG 0.005 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2292 time to fit residues: 26.0170 Evaluate side-chains 60 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 102 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN K 153 ASN K 180 HIS L 80 GLN ** M 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.200 Angle : 0.640 6.734 4674 Z= 0.338 Chirality : 0.044 0.294 508 Planarity : 0.004 0.038 603 Dihedral : 4.760 24.522 452 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.66 % Allowed : 16.90 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.56 (0.41), residues: 413 helix: 1.17 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.49 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 53 HIS 0.009 0.002 HIS K 172 PHE 0.019 0.002 PHE M 15 TYR 0.022 0.002 TYR M 85 ARG 0.005 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 0.1875 time to fit residues: 19.9894 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0338 time to fit residues: 0.9976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3456 Z= 0.268 Angle : 0.659 8.512 4674 Z= 0.350 Chirality : 0.046 0.299 508 Planarity : 0.005 0.042 603 Dihedral : 4.709 24.228 452 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.51 % Allowed : 18.87 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.07 (0.41), residues: 413 helix: 1.54 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.27 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 12 HIS 0.008 0.002 HIS K 172 PHE 0.017 0.002 PHE K 24 TYR 0.030 0.002 TYR M 85 ARG 0.007 0.001 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 74 average time/residue: 0.1942 time to fit residues: 16.9192 Evaluate side-chains 70 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0861 time to fit residues: 1.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3456 Z= 0.184 Angle : 0.652 10.407 4674 Z= 0.329 Chirality : 0.045 0.285 508 Planarity : 0.004 0.038 603 Dihedral : 4.445 23.079 452 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.25 % Allowed : 19.72 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.54 (0.41), residues: 413 helix: 1.83 (0.29), residues: 292 sheet: None (None), residues: 0 loop : -1.02 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 12 HIS 0.007 0.002 HIS K 172 PHE 0.012 0.001 PHE K 24 TYR 0.028 0.002 TYR M 85 ARG 0.009 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 77 average time/residue: 0.1810 time to fit residues: 16.5011 Evaluate side-chains 60 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0397 time to fit residues: 0.7642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3456 Z= 0.294 Angle : 0.679 13.017 4674 Z= 0.354 Chirality : 0.043 0.155 508 Planarity : 0.004 0.040 603 Dihedral : 4.691 22.609 452 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.38 % Allowed : 21.69 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.33 (0.41), residues: 413 helix: 1.71 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -1.12 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 33 HIS 0.008 0.002 HIS K 172 PHE 0.017 0.002 PHE K 24 TYR 0.021 0.002 TYR K 26 ARG 0.008 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 0.1966 time to fit residues: 14.4394 Evaluate side-chains 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0359 time to fit residues: 0.9857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 34 ASN ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3456 Z= 0.183 Angle : 0.630 13.141 4674 Z= 0.319 Chirality : 0.041 0.171 508 Planarity : 0.004 0.038 603 Dihedral : 4.557 22.838 452 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.85 % Allowed : 22.54 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.78 (0.42), residues: 413 helix: 2.03 (0.30), residues: 285 sheet: None (None), residues: 0 loop : -0.80 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 12 HIS 0.007 0.001 HIS K 172 PHE 0.022 0.002 PHE M 15 TYR 0.018 0.001 TYR K 26 ARG 0.005 0.001 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.1936 time to fit residues: 15.8461 Evaluate side-chains 61 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0492 time to fit residues: 0.6320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.178 Angle : 0.657 13.305 4674 Z= 0.326 Chirality : 0.042 0.272 508 Planarity : 0.004 0.037 603 Dihedral : 4.338 21.174 452 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.97 % Allowed : 24.51 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.90 (0.42), residues: 413 helix: 2.04 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.55 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 176 HIS 0.005 0.001 HIS K 172 PHE 0.012 0.001 PHE L 100 TYR 0.022 0.001 TYR K 157 ARG 0.004 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1824 time to fit residues: 15.6112 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0359 time to fit residues: 0.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3456 Z= 0.157 Angle : 0.625 14.111 4674 Z= 0.309 Chirality : 0.040 0.201 508 Planarity : 0.004 0.043 603 Dihedral : 4.140 18.588 452 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.85 % Allowed : 25.35 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.41), residues: 413 helix: 2.14 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.54 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 12 HIS 0.004 0.001 HIS K 172 PHE 0.017 0.001 PHE M 15 TYR 0.018 0.001 TYR K 26 ARG 0.005 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.1817 time to fit residues: 15.2475 Evaluate side-chains 59 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0440 time to fit residues: 0.6131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 130 ASN M 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.173 Angle : 0.673 13.719 4674 Z= 0.329 Chirality : 0.040 0.208 508 Planarity : 0.004 0.037 603 Dihedral : 4.106 17.917 452 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.56 % Allowed : 27.32 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.99 (0.42), residues: 413 helix: 2.11 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.52 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 103 HIS 0.006 0.001 HIS K 158 PHE 0.010 0.001 PHE M 15 TYR 0.014 0.001 TYR K 157 ARG 0.004 0.001 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.1908 time to fit residues: 14.1424 Evaluate side-chains 60 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0368 time to fit residues: 0.6258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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: 0.7943 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3456 Z= 0.186 Angle : 0.685 14.201 4674 Z= 0.332 Chirality : 0.041 0.207 508 Planarity : 0.004 0.037 603 Dihedral : 4.101 18.410 452 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.56 % Allowed : 28.45 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.06 (0.41), residues: 413 helix: 2.16 (0.29), residues: 287 sheet: None (None), residues: 0 loop : -0.49 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 103 HIS 0.004 0.001 HIS K 172 PHE 0.028 0.002 PHE L 76 TYR 0.018 0.001 TYR K 26 ARG 0.004 0.001 ARG K 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.1905 time to fit residues: 14.9142 Evaluate side-chains 61 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0379 time to fit residues: 0.6540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.076736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067456 restraints weight = 20161.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.068690 restraints weight = 10717.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069449 restraints weight = 6612.368| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3456 Z= 0.206 Angle : 0.684 14.322 4674 Z= 0.337 Chirality : 0.042 0.203 508 Planarity : 0.004 0.037 603 Dihedral : 4.176 17.716 452 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.41 % Allowed : 28.73 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.14 (0.41), residues: 413 helix: 2.25 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.54 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 176 HIS 0.003 0.001 HIS K 172 PHE 0.018 0.002 PHE L 76 TYR 0.011 0.001 TYR K 145 ARG 0.003 0.001 ARG K 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.73 seconds wall clock time: 30 minutes 45.71 seconds (1845.71 seconds total)