Starting phenix.real_space_refine on Thu Dec 7 18:19:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/12_2023/8h9n_34574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/12_2023/8h9n_34574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/12_2023/8h9n_34574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/12_2023/8h9n_34574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/12_2023/8h9n_34574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/12_2023/8h9n_34574.pdb" } resolution = 3.56 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= 0.011 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 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L ASP 97": "OD1" <-> "OD2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 96": "OD1" <-> "OD2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M PHE 139": "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: 2.37, per 1000 atoms: 0.70 Number of scatterers: 3381 At special positions: 0 Unit cell: (81.03, 96.36, 207.32, 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: 1.33 Conformation dependent library (CDL) restraints added in 618.8 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: 15 helices and 1 sheets defined 72.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.900A 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 Processing helix chain 'K' and resid 194 through 206 removed outlier: 3.789A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.318A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.690A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) 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: 3.896A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.690A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.662A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 237 hydrogen bonds defined for protein. 705 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: 0.85 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1078 1.34 - 1.45: 470 1.45 - 1.57: 1887 1.57 - 1.69: 0 1.69 - 1.80: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N LEU M 76 " pdb=" CA LEU M 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.19e+00 bond pdb=" N LYS K 168 " pdb=" CA LYS K 168 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.89e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.441 0.065 3.90e-02 6.57e+02 2.79e+00 bond pdb=" CB THR K 139 " pdb=" CG2 THR K 139 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.13: 88 106.13 - 113.13: 1864 113.13 - 120.12: 1388 120.12 - 127.11: 1297 127.11 - 134.11: 37 Bond angle restraints: 4674 Sorted by residual: angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.31 114.62 5.69 1.52e+00 4.33e-01 1.40e+01 angle pdb=" C LYS K 72 " pdb=" N LYS K 73 " pdb=" CA LYS K 73 " ideal model delta sigma weight residual 121.80 114.95 6.85 2.16e+00 2.14e-01 1.01e+01 angle pdb=" N ARG K 121 " pdb=" CA ARG K 121 " pdb=" C ARG K 121 " ideal model delta sigma weight residual 111.75 115.44 -3.69 1.28e+00 6.10e-01 8.31e+00 angle pdb=" C ILE K 174 " pdb=" N ASN K 175 " pdb=" CA ASN K 175 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.24e+00 angle pdb=" CA LEU K 117 " pdb=" CB LEU K 117 " pdb=" CG LEU K 117 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1847 16.70 - 33.39: 210 33.39 - 50.09: 40 50.09 - 66.79: 12 66.79 - 83.49: 4 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 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 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+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 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 220 0.029 - 0.058: 170 0.058 - 0.087: 67 0.087 - 0.116: 31 0.116 - 0.145: 20 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA VAL M 80 " pdb=" N VAL M 80 " pdb=" C VAL M 80 " pdb=" CB VAL M 80 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA PHE K 58 " pdb=" N PHE K 58 " pdb=" C PHE K 58 " pdb=" CB PHE K 58 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO K 76 " pdb=" N PRO K 76 " pdb=" C PRO K 76 " pdb=" CB PRO K 76 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE M 69 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE M 69 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE M 69 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU M 70 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE K 159 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE K 159 " -0.011 2.00e-02 2.50e+03 pdb=" N SER K 160 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 139 " 0.014 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE M 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE M 139 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE M 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE M 139 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE M 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE M 139 " 0.002 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 295 2.72 - 3.27: 3535 3.27 - 3.81: 5368 3.81 - 4.36: 5909 4.36 - 4.90: 10125 Nonbonded interactions: 25232 Sorted by model distance: nonbonded pdb=" O VAL K 181 " pdb=" OG SER K 184 " model vdw 2.178 2.440 nonbonded pdb=" NZ LYS K 84 " pdb=" OE1 GLU K 87 " model vdw 2.254 2.520 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.272 2.520 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASP K 126 " pdb=" NH2 ARG K 129 " model vdw 2.278 2.520 ... (remaining 25227 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: 5.640 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: 26.850 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 14.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.007 0.065 3456 Z= 0.443 Angle : 0.878 9.610 4674 Z= 0.496 Chirality : 0.052 0.145 508 Planarity : 0.006 0.040 603 Dihedral : 15.253 83.485 1299 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: -2.28 (0.34), residues: 413 helix: -1.09 (0.25), residues: 285 sheet: None (None), residues: 0 loop : -2.19 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 176 HIS 0.006 0.003 HIS K 158 PHE 0.030 0.003 PHE M 139 TYR 0.020 0.003 TYR K 140 ARG 0.004 0.001 ARG M 40 *********************** 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 117 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2336 time to fit residues: 31.1018 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5882 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 103 HIS K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 ASN M 59 ASN M 136 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.203 Angle : 0.607 7.846 4674 Z= 0.327 Chirality : 0.041 0.143 508 Planarity : 0.006 0.045 603 Dihedral : 5.048 45.381 452 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.23 % Allowed : 13.52 % Favored : 82.25 % 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: 0.55 (0.41), residues: 413 helix: 1.29 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.80 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.016 0.002 PHE L 93 TYR 0.023 0.002 TYR M 56 ARG 0.006 0.001 ARG M 40 *********************** 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 96 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.1921 time to fit residues: 20.5323 Evaluate side-chains 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0397 time to fit residues: 1.2429 ------------------------------------------------------------------------------- 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: 8.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3456 Z= 0.279 Angle : 0.632 6.965 4674 Z= 0.341 Chirality : 0.042 0.149 508 Planarity : 0.005 0.047 603 Dihedral : 4.779 34.974 452 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.69 % Allowed : 19.72 % Favored : 78.59 % 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: 1.19 (0.43), residues: 413 helix: 1.78 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.57 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 53 HIS 0.003 0.001 HIS K 158 PHE 0.020 0.002 PHE K 24 TYR 0.016 0.002 TYR K 145 ARG 0.007 0.001 ARG K 167 *********************** 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 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 79 average time/residue: 0.2019 time to fit residues: 18.7131 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0338 time to fit residues: 0.6941 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 19 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3456 Z= 0.182 Angle : 0.564 6.335 4674 Z= 0.305 Chirality : 0.039 0.140 508 Planarity : 0.005 0.044 603 Dihedral : 4.491 27.920 452 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.97 % Allowed : 19.72 % Favored : 78.31 % 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: 1.79 (0.43), residues: 413 helix: 2.23 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -1.35 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 33 HIS 0.002 0.001 HIS K 158 PHE 0.026 0.002 PHE K 24 TYR 0.022 0.001 TYR M 85 ARG 0.006 0.001 ARG K 166 *********************** 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 83 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.2026 time to fit residues: 19.1116 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1845 time to fit residues: 1.4291 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.0470 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3456 Z= 0.214 Angle : 0.591 7.460 4674 Z= 0.317 Chirality : 0.039 0.140 508 Planarity : 0.005 0.044 603 Dihedral : 4.326 19.535 452 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 22.54 % Favored : 75.77 % 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: 1.93 (0.43), residues: 413 helix: 2.30 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.20 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 53 HIS 0.003 0.001 HIS K 158 PHE 0.018 0.002 PHE K 24 TYR 0.026 0.002 TYR M 85 ARG 0.004 0.001 ARG M 40 *********************** 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 83 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.2081 time to fit residues: 19.4756 Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0395 time to fit residues: 0.7704 ------------------------------------------------------------------------------- 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: 6.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.0020 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3456 Z= 0.171 Angle : 0.593 6.858 4674 Z= 0.311 Chirality : 0.038 0.138 508 Planarity : 0.005 0.041 603 Dihedral : 4.156 20.884 452 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.41 % Allowed : 24.51 % Favored : 74.08 % 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: 2.39 (0.43), residues: 413 helix: 2.71 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -1.01 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.018 0.001 PHE K 24 TYR 0.022 0.001 TYR M 85 ARG 0.003 0.001 ARG K 154 *********************** 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 77 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.2002 time to fit residues: 17.8961 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0447 time to fit residues: 0.8815 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3456 Z= 0.174 Angle : 0.616 8.700 4674 Z= 0.326 Chirality : 0.039 0.143 508 Planarity : 0.005 0.041 603 Dihedral : 4.044 20.629 452 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.56 % Allowed : 23.94 % Favored : 75.49 % 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: 2.70 (0.43), residues: 413 helix: 2.87 (0.29), residues: 283 sheet: None (None), residues: 0 loop : -0.75 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.014 0.001 PHE L 100 TYR 0.023 0.001 TYR M 85 ARG 0.003 0.001 ARG M 40 *********************** 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 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.1954 time to fit residues: 16.5983 Evaluate side-chains 66 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0530 time to fit residues: 0.6619 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3456 Z= 0.320 Angle : 0.691 6.778 4674 Z= 0.372 Chirality : 0.043 0.153 508 Planarity : 0.005 0.043 603 Dihedral : 4.266 20.628 452 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.25 % Allowed : 23.66 % Favored : 74.08 % 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: 2.15 (0.43), residues: 413 helix: 2.50 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -1.03 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP M 53 HIS 0.004 0.001 HIS K 180 PHE 0.015 0.002 PHE K 24 TYR 0.025 0.002 TYR M 85 ARG 0.005 0.001 ARG M 110 *********************** 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 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.1909 time to fit residues: 16.3248 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0389 time to fit residues: 0.9216 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN K 130 ASN ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4640 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= 0.191 Angle : 0.665 9.426 4674 Z= 0.355 Chirality : 0.040 0.140 508 Planarity : 0.005 0.043 603 Dihedral : 4.137 20.811 452 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.28 % Allowed : 24.51 % Favored : 75.21 % 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: 2.56 (0.43), residues: 413 helix: 2.75 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -0.79 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 176 HIS 0.002 0.001 HIS K 172 PHE 0.021 0.001 PHE K 24 TYR 0.026 0.002 TYR M 85 ARG 0.005 0.001 ARG K 154 *********************** 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 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.2018 time to fit residues: 17.1124 Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0343 time to fit residues: 0.6341 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3456 Z= 0.200 Angle : 0.664 7.633 4674 Z= 0.357 Chirality : 0.040 0.143 508 Planarity : 0.005 0.044 603 Dihedral : 4.123 20.706 452 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.28 % Allowed : 27.32 % Favored : 72.39 % 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: 2.40 (0.43), residues: 413 helix: 2.71 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.97 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.009 0.001 PHE M 139 TYR 0.027 0.001 TYR K 148 ARG 0.004 0.001 ARG K 154 ********************** 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 68 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1811 time to fit residues: 14.6558 Evaluate side-chains 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5750 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.139422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.122145 restraints weight = 8777.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.122991 restraints weight = 4387.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.124436 restraints weight = 2526.611| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4923 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= 0.220 Angle : 0.707 10.400 4674 Z= 0.371 Chirality : 0.040 0.143 508 Planarity : 0.005 0.045 603 Dihedral : 4.150 20.687 452 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.69 % Allowed : 27.32 % 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: 2.39 (0.43), residues: 413 helix: 2.71 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.98 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.009 0.001 PHE M 139 TYR 0.023 0.001 TYR M 85 ARG 0.007 0.001 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.18 seconds wall clock time: 27 minutes 15.79 seconds (1635.79 seconds total)