Starting phenix.real_space_refine on Mon Sep 23 11:54:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/09_2024/6yj5_10816_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/09_2024/6yj5_10816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/09_2024/6yj5_10816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/09_2024/6yj5_10816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/09_2024/6yj5_10816_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/09_2024/6yj5_10816_neut.cif" } resolution = 3.5 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= 0.004 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 5 5.16 5 C 1308 2.51 5 N 352 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2061 Number of models: 1 Model: "" Number of chains: 1 Chain: "q" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2061 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 280} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 168 Time building chain proxies: 3.19, per 1000 atoms: 1.55 Number of scatterers: 2061 At special positions: 0 Unit cell: (55.915, 72.795, 61.19, 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 5 16.00 O 396 8.00 N 352 7.00 C 1308 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 - 3.00 Amino acid : True - 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: 0.42 Conformation dependent library (CDL) restraints added in 284.3 milliseconds 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 34.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'q' and resid 6 through 15 removed outlier: 3.583A pdb=" N LEU q 10 " --> pdb=" O SER q 6 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA q 11 " --> pdb=" O PRO q 7 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS q 12 " --> pdb=" O ALA q 8 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER q 15 " --> pdb=" O ALA q 11 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 43 removed outlier: 3.566A pdb=" N MET q 43 " --> pdb=" O TYR q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 54 through 59 removed outlier: 3.924A pdb=" N ASN q 59 " --> pdb=" O ILE q 55 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 79 Processing helix chain 'q' and resid 100 through 110 removed outlier: 3.763A pdb=" N VAL q 104 " --> pdb=" O GLY q 100 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 120 through 126 removed outlier: 3.619A pdb=" N TYR q 124 " --> pdb=" O GLY q 120 " (cutoff:3.500A) Processing helix chain 'q' and resid 169 through 175 Processing helix chain 'q' and resid 176 through 179 Processing helix chain 'q' and resid 181 through 185 removed outlier: 3.547A pdb=" N GLY q 184 " --> pdb=" O ASN q 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 186 through 191 removed outlier: 3.526A pdb=" N VAL q 191 " --> pdb=" O ILE q 187 " (cutoff:3.500A) Processing helix chain 'q' and resid 237 through 247 Processing helix chain 'q' and resid 260 through 264 removed outlier: 3.504A pdb=" N VAL q 264 " --> pdb=" O GLY q 261 " (cutoff:3.500A) Processing helix chain 'q' and resid 265 through 266 No H-bonds generated for 'chain 'q' and resid 265 through 266' Processing helix chain 'q' and resid 267 through 277 removed outlier: 4.961A pdb=" N LEU q 273 " --> pdb=" O ILE q 269 " (cutoff:3.500A) Processing helix chain 'q' and resid 290 through 297 Processing sheet with id=AA1, first strand: chain 'q' and resid 3 through 5 removed outlier: 3.556A pdb=" N LYS q 3 " --> pdb=" O VAL q 115 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE q 89 " --> pdb=" O GLN q 116 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU q 118 " --> pdb=" O ILE q 89 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL q 91 " --> pdb=" O LEU q 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'q' and resid 192 through 193 removed outlier: 6.281A pdb=" N THR q 192 " --> pdb=" O ILE q 257 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE q 256 " --> pdb=" O ALA q 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 44 hydrogen bonds defined for protein. 120 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: 0.37 Time building geometry restraints manager: 0.51 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: 698 1.34 - 1.46: 450 1.46 - 1.57: 950 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 2106 Sorted by residual: bond pdb=" CA GLY q 140 " pdb=" C GLY q 140 " ideal model delta sigma weight residual 1.516 1.498 0.019 1.31e-02 5.83e+03 2.04e+00 bond pdb=" C MET q 43 " pdb=" N LYS q 44 " ideal model delta sigma weight residual 1.333 1.312 0.020 1.52e-02 4.33e+03 1.81e+00 bond pdb=" CB PRO q 69 " pdb=" CG PRO q 69 " ideal model delta sigma weight residual 1.492 1.428 0.064 5.00e-02 4.00e+02 1.66e+00 bond pdb=" CG PRO q 48 " pdb=" CD PRO q 48 " ideal model delta sigma weight residual 1.503 1.461 0.042 3.40e-02 8.65e+02 1.53e+00 bond pdb=" CG LEU q 51 " pdb=" CD1 LEU q 51 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 ... (remaining 2101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 2500 1.15 - 2.30: 316 2.30 - 3.45: 55 3.45 - 4.60: 9 4.60 - 5.75: 9 Bond angle restraints: 2889 Sorted by residual: angle pdb=" N GLY q 140 " pdb=" CA GLY q 140 " pdb=" C GLY q 140 " ideal model delta sigma weight residual 114.25 110.04 4.21 1.30e+00 5.92e-01 1.05e+01 angle pdb=" N PHE q 226 " pdb=" CA PHE q 226 " pdb=" CB PHE q 226 " ideal model delta sigma weight residual 110.39 107.68 2.71 9.50e-01 1.11e+00 8.15e+00 angle pdb=" N LEU q 14 " pdb=" CA LEU q 14 " pdb=" C LEU q 14 " ideal model delta sigma weight residual 111.36 114.40 -3.04 1.09e+00 8.42e-01 7.78e+00 angle pdb=" N ASN q 232 " pdb=" CA ASN q 232 " pdb=" C ASN q 232 " ideal model delta sigma weight residual 110.80 116.16 -5.36 2.13e+00 2.20e-01 6.33e+00 angle pdb=" C GLU q 231 " pdb=" N ASN q 232 " pdb=" CA ASN q 232 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.80e+00 ... (remaining 2884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1145 17.95 - 35.91: 74 35.91 - 53.86: 11 53.86 - 71.81: 2 71.81 - 89.77: 1 Dihedral angle restraints: 1233 sinusoidal: 355 harmonic: 878 Sorted by residual: dihedral pdb=" CA GLN q 72 " pdb=" C GLN q 72 " pdb=" N THR q 73 " pdb=" CA THR q 73 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ILE q 269 " pdb=" C ILE q 269 " pdb=" N ASP q 270 " pdb=" CA ASP q 270 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR q 138 " pdb=" C THR q 138 " pdb=" N TRP q 139 " pdb=" CA TRP q 139 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 163 0.030 - 0.060: 107 0.060 - 0.089: 40 0.089 - 0.119: 18 0.119 - 0.148: 6 Chirality restraints: 334 Sorted by residual: chirality pdb=" CA ILE q 130 " pdb=" N ILE q 130 " pdb=" C ILE q 130 " pdb=" CB ILE q 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA PRO q 101 " pdb=" N PRO q 101 " pdb=" C PRO q 101 " pdb=" CB PRO q 101 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE q 257 " pdb=" N ILE q 257 " pdb=" C ILE q 257 " pdb=" CB ILE q 257 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 331 not shown) Planarity restraints: 387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG q 197 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO q 198 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO q 198 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO q 198 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY q 100 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO q 101 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO q 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO q 101 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE q 74 " -0.013 2.00e-02 2.50e+03 1.09e-02 2.07e+00 pdb=" CG PHE q 74 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE q 74 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE q 74 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE q 74 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE q 74 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE q 74 " -0.006 2.00e-02 2.50e+03 ... (remaining 384 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 168 2.73 - 3.27: 2199 3.27 - 3.81: 3086 3.81 - 4.36: 3655 4.36 - 4.90: 6026 Nonbonded interactions: 15134 Sorted by model distance: nonbonded pdb=" NZ LYS q 108 " pdb=" OE2 GLU q 274 " model vdw 2.183 3.120 nonbonded pdb=" N SER q 2 " pdb=" OE1 GLU q 274 " model vdw 2.206 3.120 nonbonded pdb=" O ARG q 102 " pdb=" OG1 THR q 106 " model vdw 2.246 3.040 nonbonded pdb=" NH2 ARG q 102 " pdb=" OD2 ASP q 288 " model vdw 2.261 3.120 nonbonded pdb=" N GLU q 9 " pdb=" OE1 GLU q 9 " model vdw 2.321 3.120 ... (remaining 15129 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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:4.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 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 0.064 2106 Z= 0.492 Angle : 0.874 5.754 2889 Z= 0.505 Chirality : 0.048 0.148 334 Planarity : 0.005 0.043 387 Dihedral : 13.190 89.768 669 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.38), residues: 304 helix: -4.08 (0.28), residues: 88 sheet: -2.97 (0.77), residues: 28 loop : -3.29 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP q 142 HIS 0.001 0.001 HIS q 112 PHE 0.024 0.002 PHE q 74 TYR 0.008 0.002 TYR q 124 ARG 0.006 0.001 ARG q 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: q 4 LEU cc_start: 0.6754 (pp) cc_final: 0.6549 (pp) REVERT: q 6 SER cc_start: 0.7911 (m) cc_final: 0.7182 (p) REVERT: q 89 ILE cc_start: 0.8145 (pt) cc_final: 0.7855 (mt) REVERT: q 114 ASN cc_start: 0.6728 (m110) cc_final: 0.6156 (m110) REVERT: q 117 PHE cc_start: 0.8105 (t80) cc_final: 0.7728 (t80) REVERT: q 163 ARG cc_start: 0.6876 (ptp90) cc_final: 0.6622 (ptp90) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1540 time to fit residues: 7.7023 Evaluate side-chains 32 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.6046 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2106 Z= 0.180 Angle : 0.608 4.763 2889 Z= 0.324 Chirality : 0.050 0.141 334 Planarity : 0.005 0.045 387 Dihedral : 5.525 19.119 320 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 1.23 % Allowed : 8.59 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.43), residues: 304 helix: -2.67 (0.41), residues: 91 sheet: -1.97 (0.76), residues: 32 loop : -2.36 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 291 HIS 0.001 0.001 HIS q 112 PHE 0.016 0.001 PHE q 74 TYR 0.013 0.002 TYR q 52 ARG 0.002 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.252 Fit side-chains REVERT: q 4 LEU cc_start: 0.7058 (pp) cc_final: 0.6842 (pp) REVERT: q 18 GLU cc_start: 0.7135 (mp0) cc_final: 0.5629 (tp30) REVERT: q 39 TYR cc_start: 0.7501 (t80) cc_final: 0.7240 (t80) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1299 time to fit residues: 6.1152 Evaluate side-chains 29 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 0.0870 chunk 27 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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: 0.6081 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2106 Z= 0.159 Angle : 0.553 4.789 2889 Z= 0.295 Chirality : 0.049 0.126 334 Planarity : 0.005 0.048 387 Dihedral : 4.891 18.099 320 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.84 % Allowed : 12.27 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.46), residues: 304 helix: -2.13 (0.46), residues: 94 sheet: -1.19 (0.85), residues: 32 loop : -1.95 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP q 105 HIS 0.001 0.001 HIS q 112 PHE 0.013 0.001 PHE q 74 TYR 0.008 0.001 TYR q 52 ARG 0.007 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.251 Fit side-chains REVERT: q 9 GLU cc_start: 0.5623 (mp0) cc_final: 0.5329 (mp0) REVERT: q 70 SER cc_start: 0.8178 (m) cc_final: 0.7770 (p) REVERT: q 72 GLN cc_start: 0.7206 (mt0) cc_final: 0.6062 (mp10) REVERT: q 89 ILE cc_start: 0.8096 (pt) cc_final: 0.7828 (mt) REVERT: q 99 SER cc_start: 0.7615 (t) cc_final: 0.7343 (m) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.1164 time to fit residues: 5.5412 Evaluate side-chains 25 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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: 0.6177 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2106 Z= 0.263 Angle : 0.621 5.645 2889 Z= 0.325 Chirality : 0.050 0.128 334 Planarity : 0.006 0.049 387 Dihedral : 5.323 18.782 320 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.61 % Allowed : 17.18 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.46), residues: 304 helix: -1.94 (0.46), residues: 96 sheet: -1.03 (0.90), residues: 32 loop : -1.98 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP q 105 HIS 0.004 0.002 HIS q 112 PHE 0.013 0.002 PHE q 74 TYR 0.008 0.001 TYR q 157 ARG 0.008 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.258 Fit side-chains REVERT: q 18 GLU cc_start: 0.7219 (mp0) cc_final: 0.6754 (mp0) REVERT: q 72 GLN cc_start: 0.7310 (mt0) cc_final: 0.6271 (mp10) REVERT: q 89 ILE cc_start: 0.8131 (pt) cc_final: 0.7821 (mp) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0765 time to fit residues: 3.5335 Evaluate side-chains 29 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.0020 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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: 0.6168 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2106 Z= 0.186 Angle : 0.550 4.507 2889 Z= 0.290 Chirality : 0.048 0.122 334 Planarity : 0.006 0.057 387 Dihedral : 4.838 18.215 320 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.91 % Allowed : 15.34 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.47), residues: 304 helix: -1.61 (0.50), residues: 94 sheet: -0.91 (0.94), residues: 32 loop : -1.88 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 291 HIS 0.001 0.001 HIS q 112 PHE 0.014 0.001 PHE q 74 TYR 0.005 0.001 TYR q 157 ARG 0.007 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.232 Fit side-chains REVERT: q 9 GLU cc_start: 0.5591 (mp0) cc_final: 0.5355 (mp0) REVERT: q 17 LYS cc_start: 0.5151 (mmpt) cc_final: 0.4888 (mtmt) REVERT: q 72 GLN cc_start: 0.7421 (mt0) cc_final: 0.6211 (mp10) REVERT: q 87 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7815 (m) REVERT: q 269 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6737 (pt) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 0.0937 time to fit residues: 4.7216 Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 2 optimal weight: 0.0020 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 0.5306 ------------------------------------------------------------------------------- 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: 0.6160 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2106 Z= 0.168 Angle : 0.536 4.804 2889 Z= 0.281 Chirality : 0.047 0.121 334 Planarity : 0.005 0.056 387 Dihedral : 4.644 18.526 320 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.07 % Allowed : 16.56 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.47), residues: 304 helix: -1.60 (0.49), residues: 95 sheet: -0.74 (0.95), residues: 32 loop : -1.78 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 291 HIS 0.001 0.001 HIS q 112 PHE 0.014 0.001 PHE q 74 TYR 0.005 0.001 TYR q 92 ARG 0.007 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.233 Fit side-chains REVERT: q 9 GLU cc_start: 0.5612 (mp0) cc_final: 0.5400 (mp0) REVERT: q 17 LYS cc_start: 0.5050 (mmpt) cc_final: 0.4820 (mtmt) REVERT: q 72 GLN cc_start: 0.7395 (mt0) cc_final: 0.6212 (mp10) REVERT: q 87 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7796 (m) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.0936 time to fit residues: 4.0017 Evaluate side-chains 35 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain q residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.6223 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 2106 Z= 0.328 Angle : 0.626 5.385 2889 Z= 0.326 Chirality : 0.050 0.139 334 Planarity : 0.006 0.056 387 Dihedral : 5.494 20.082 320 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.68 % Allowed : 16.56 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.46), residues: 304 helix: -1.83 (0.48), residues: 95 sheet: -0.52 (0.95), residues: 27 loop : -1.86 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 291 HIS 0.003 0.002 HIS q 112 PHE 0.017 0.002 PHE q 74 TYR 0.007 0.002 TYR q 92 ARG 0.006 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.228 Fit side-chains REVERT: q 9 GLU cc_start: 0.5745 (mp0) cc_final: 0.5465 (mp0) REVERT: q 17 LYS cc_start: 0.5433 (mmpt) cc_final: 0.4687 (mtmt) REVERT: q 72 GLN cc_start: 0.7371 (mt0) cc_final: 0.6115 (mp10) REVERT: q 87 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7550 (p) REVERT: q 267 CYS cc_start: 0.7360 (m) cc_final: 0.6785 (m) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.1359 time to fit residues: 5.7023 Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain q residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0870 chunk 22 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2106 Z= 0.147 Angle : 0.526 4.680 2889 Z= 0.274 Chirality : 0.047 0.126 334 Planarity : 0.005 0.060 387 Dihedral : 4.571 18.318 320 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.07 % Allowed : 17.18 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.46), residues: 304 helix: -1.36 (0.54), residues: 83 sheet: -1.13 (0.89), residues: 32 loop : -1.69 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP q 291 HIS 0.001 0.000 HIS q 112 PHE 0.011 0.001 PHE q 74 TYR 0.005 0.001 TYR q 92 ARG 0.005 0.001 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.392 Fit side-chains REVERT: q 17 LYS cc_start: 0.5365 (mmpt) cc_final: 0.4988 (ptpt) REVERT: q 72 GLN cc_start: 0.7266 (mt0) cc_final: 0.6090 (mp10) REVERT: q 87 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7609 (m) REVERT: q 165 GLU cc_start: 0.7021 (mp0) cc_final: 0.6749 (mm-30) REVERT: q 259 MET cc_start: 0.6096 (ptm) cc_final: 0.5469 (ptp) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.1277 time to fit residues: 5.6244 Evaluate side-chains 31 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain q residue 89 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.6225 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 2106 Z= 0.354 Angle : 0.628 4.990 2889 Z= 0.324 Chirality : 0.050 0.208 334 Planarity : 0.005 0.053 387 Dihedral : 5.274 18.312 320 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.07 % Allowed : 18.40 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.46), residues: 304 helix: -1.69 (0.49), residues: 89 sheet: -0.26 (0.99), residues: 25 loop : -1.73 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 291 HIS 0.005 0.003 HIS q 112 PHE 0.016 0.002 PHE q 74 TYR 0.014 0.002 TYR q 124 ARG 0.005 0.001 ARG q 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.207 Fit side-chains REVERT: q 9 GLU cc_start: 0.5723 (mp0) cc_final: 0.5467 (mp0) REVERT: q 17 LYS cc_start: 0.5633 (mmpt) cc_final: 0.5078 (ptpt) REVERT: q 72 GLN cc_start: 0.7342 (mt0) cc_final: 0.6098 (mp10) REVERT: q 87 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7819 (m) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.1399 time to fit residues: 5.3758 Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain q residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.0170 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.6173 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2106 Z= 0.178 Angle : 0.546 4.760 2889 Z= 0.283 Chirality : 0.048 0.166 334 Planarity : 0.005 0.058 387 Dihedral : 4.666 17.610 320 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.07 % Allowed : 18.40 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.47), residues: 304 helix: -1.30 (0.54), residues: 83 sheet: -1.29 (0.86), residues: 32 loop : -1.56 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP q 291 HIS 0.001 0.001 HIS q 112 PHE 0.013 0.001 PHE q 74 TYR 0.006 0.001 TYR q 124 ARG 0.004 0.001 ARG q 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.232 Fit side-chains REVERT: q 17 LYS cc_start: 0.5555 (mmpt) cc_final: 0.5037 (ptpt) REVERT: q 72 GLN cc_start: 0.7221 (mt0) cc_final: 0.6057 (mp10) REVERT: q 87 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7908 (m) REVERT: q 228 GLU cc_start: 0.6926 (mt-10) cc_final: 0.5627 (mm-30) REVERT: q 259 MET cc_start: 0.6321 (ptm) cc_final: 0.5682 (ptp) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.0950 time to fit residues: 3.8284 Evaluate side-chains 32 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain q residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.171930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.157771 restraints weight = 2982.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.158610 restraints weight = 2317.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159479 restraints weight = 1981.695| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2106 Z= 0.316 Angle : 0.617 4.814 2889 Z= 0.317 Chirality : 0.050 0.189 334 Planarity : 0.005 0.052 387 Dihedral : 5.180 18.221 320 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 3.68 % Allowed : 17.79 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.47), residues: 304 helix: -1.46 (0.52), residues: 83 sheet: -0.46 (1.00), residues: 25 loop : -1.66 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP q 291 HIS 0.004 0.003 HIS q 112 PHE 0.014 0.002 PHE q 74 TYR 0.010 0.002 TYR q 124 ARG 0.006 0.001 ARG q 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1046.54 seconds wall clock time: 23 minutes 24.18 seconds (1404.18 seconds total)