Starting phenix.real_space_refine on Mon Feb 10 19:59:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yj5_10816/02_2025/6yj5_10816_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yj5_10816/02_2025/6yj5_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/cci-nas-00/data/ceres_data/6yj5_10816/02_2025/6yj5_10816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yj5_10816/02_2025/6yj5_10816.map" model { file = "/net/cci-nas-00/data/ceres_data/6yj5_10816/02_2025/6yj5_10816_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yj5_10816/02_2025/6yj5_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-5592/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: 3.23, per 1000 atoms: 1.57 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: 0.53 Conformation dependent library (CDL) restraints added in 328.5 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: 0.24 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: 0.46 Time building geometry restraints manager: 0.64 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: 4.500 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.211 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: 0.1588 time to fit residues: 7.9061 Evaluate side-chains 32 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.191598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.178683 restraints weight = 2853.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180116 restraints weight = 2056.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181107 restraints weight = 1610.358| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 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 to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.220 Fit side-chains REVERT: q 18 GLU cc_start: 0.6960 (mp0) cc_final: 0.6027 (tp30) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1265 time to fit residues: 5.9482 Evaluate side-chains 29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 29 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0000 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.186091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174812 restraints weight = 3098.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175440 restraints weight = 2459.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.175709 restraints weight = 2115.913| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3195 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= 0.172 Angle : 0.569 4.648 2889 Z= 0.301 Chirality : 0.048 0.128 334 Planarity : 0.005 0.049 387 Dihedral : 5.030 18.572 320 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.23 % Allowed : 12.27 % Favored : 86.50 % 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: -2.92 (0.46), residues: 304 helix: -2.17 (0.46), residues: 94 sheet: -1.25 (0.84), residues: 32 loop : -1.96 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP q 105 HIS 0.001 0.001 HIS q 112 PHE 0.013 0.001 PHE q 74 TYR 0.007 0.001 TYR q 157 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 to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.236 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1125 time to fit residues: 5.2861 Evaluate side-chains 23 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.183756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170226 restraints weight = 2911.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.171405 restraints weight = 2251.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171946 restraints weight = 1858.719| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2106 Z= 0.172 Angle : 0.563 5.915 2889 Z= 0.291 Chirality : 0.048 0.127 334 Planarity : 0.005 0.050 387 Dihedral : 4.794 18.179 320 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.45 % Allowed : 14.72 % Favored : 82.82 % 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: -2.53 (0.47), residues: 304 helix: -1.64 (0.50), residues: 89 sheet: -0.81 (0.89), residues: 32 loop : -1.91 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP q 105 HIS 0.005 0.003 HIS q 112 PHE 0.014 0.001 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 to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.237 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.0956 time to fit residues: 4.1306 Evaluate side-chains 29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 73 THR 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 24 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.177992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164353 restraints weight = 3017.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164958 restraints weight = 2378.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165929 restraints weight = 2072.182| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4611 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= 0.226 Angle : 0.596 6.867 2889 Z= 0.309 Chirality : 0.049 0.125 334 Planarity : 0.005 0.053 387 Dihedral : 5.093 19.013 320 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.45 % Allowed : 16.56 % Favored : 80.98 % 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: -2.52 (0.46), residues: 304 helix: -1.75 (0.48), residues: 100 sheet: -0.13 (1.00), residues: 28 loop : -1.93 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 291 HIS 0.006 0.004 HIS q 112 PHE 0.011 0.002 PHE q 74 TYR 0.007 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 33 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.219 Fit side-chains REVERT: q 28 LEU cc_start: 0.7732 (mt) cc_final: 0.7523 (mt) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.1024 time to fit residues: 4.1143 Evaluate side-chains 24 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.180966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167239 restraints weight = 2956.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.168252 restraints weight = 2289.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169206 restraints weight = 1924.355| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4842 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= 0.155 Angle : 0.528 4.693 2889 Z= 0.277 Chirality : 0.047 0.122 334 Planarity : 0.005 0.057 387 Dihedral : 4.599 17.500 320 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.23 % Allowed : 17.79 % Favored : 80.98 % 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: -2.29 (0.46), residues: 304 helix: -1.59 (0.49), residues: 95 sheet: -0.01 (1.03), residues: 28 loop : -1.77 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 291 HIS 0.003 0.002 HIS q 112 PHE 0.010 0.001 PHE q 74 TYR 0.004 0.001 TYR q 52 ARG 0.006 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 27 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.231 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.1019 time to fit residues: 3.4856 Evaluate side-chains 26 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.180020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165836 restraints weight = 2996.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166766 restraints weight = 2340.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.167685 restraints weight = 1989.778| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2106 Z= 0.181 Angle : 0.531 4.724 2889 Z= 0.275 Chirality : 0.047 0.162 334 Planarity : 0.005 0.058 387 Dihedral : 4.583 17.576 320 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.45 % Allowed : 16.56 % Favored : 80.98 % 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: -2.22 (0.46), residues: 304 helix: -1.66 (0.48), residues: 99 sheet: -0.19 (0.99), residues: 28 loop : -1.59 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 291 HIS 0.004 0.002 HIS q 112 PHE 0.011 0.001 PHE q 74 TYR 0.006 0.001 TYR q 124 ARG 0.007 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 31 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.230 Fit side-chains REVERT: q 28 LEU cc_start: 0.7660 (mt) cc_final: 0.7400 (mt) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.1214 time to fit residues: 4.5170 Evaluate side-chains 30 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 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 79 THR 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 14 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.177522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.163105 restraints weight = 3002.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164252 restraints weight = 2324.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164941 restraints weight = 1936.767| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5290 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= 0.217 Angle : 0.562 4.742 2889 Z= 0.290 Chirality : 0.048 0.182 334 Planarity : 0.005 0.057 387 Dihedral : 4.737 16.129 320 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.45 % Allowed : 16.56 % Favored : 80.98 % 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: -2.18 (0.47), residues: 304 helix: -1.56 (0.50), residues: 93 sheet: -0.28 (0.97), residues: 28 loop : -1.61 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 291 HIS 0.004 0.003 HIS q 112 PHE 0.010 0.001 PHE q 74 TYR 0.007 0.001 TYR q 124 ARG 0.007 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 33 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.227 Fit side-chains REVERT: q 28 LEU cc_start: 0.7737 (mt) cc_final: 0.7518 (mt) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.1325 time to fit residues: 5.2517 Evaluate side-chains 31 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.0000 overall best weight: 0.3702 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.181913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168171 restraints weight = 2979.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169427 restraints weight = 2264.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170086 restraints weight = 1847.277| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2106 Z= 0.141 Angle : 0.508 4.658 2889 Z= 0.263 Chirality : 0.047 0.160 334 Planarity : 0.005 0.059 387 Dihedral : 4.381 16.029 320 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.61 % Allowed : 19.63 % 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: -1.94 (0.47), residues: 304 helix: -1.16 (0.54), residues: 83 sheet: -0.30 (0.93), residues: 28 loop : -1.55 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 291 HIS 0.002 0.001 HIS q 112 PHE 0.010 0.001 PHE q 74 TYR 0.004 0.001 TYR q 124 ARG 0.006 0.001 ARG q 13 *********************** 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 29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.235 Fit side-chains REVERT: q 28 LEU cc_start: 0.7611 (mt) cc_final: 0.7389 (mt) REVERT: q 39 TYR cc_start: 0.8278 (t80) cc_final: 0.8074 (t80) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.1277 time to fit residues: 4.4037 Evaluate side-chains 26 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 0.0040 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.181767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168227 restraints weight = 2917.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.169209 restraints weight = 2244.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170079 restraints weight = 1868.946| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2106 Z= 0.149 Angle : 0.512 4.692 2889 Z= 0.264 Chirality : 0.046 0.160 334 Planarity : 0.005 0.058 387 Dihedral : 4.257 16.531 320 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.61 % Allowed : 18.40 % Favored : 80.98 % 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: -1.91 (0.47), residues: 304 helix: -1.23 (0.53), residues: 87 sheet: -0.41 (0.94), residues: 28 loop : -1.44 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 291 HIS 0.002 0.002 HIS q 112 PHE 0.009 0.001 PHE q 235 TYR 0.005 0.001 TYR q 124 ARG 0.007 0.001 ARG q 13 ********************** 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 29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.230 Fit side-chains REVERT: q 28 LEU cc_start: 0.7586 (mt) cc_final: 0.7369 (mt) REVERT: q 39 TYR cc_start: 0.8275 (t80) cc_final: 0.8065 (t80) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1356 time to fit residues: 4.7941 Evaluate side-chains 28 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 0.0670 chunk 1 optimal weight: 0.0060 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.2934 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167236 restraints weight = 2997.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168341 restraints weight = 2286.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168784 restraints weight = 1906.122| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2106 Z= 0.135 Angle : 0.507 4.706 2889 Z= 0.263 Chirality : 0.046 0.157 334 Planarity : 0.005 0.058 387 Dihedral : 4.127 16.378 320 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.61 % Allowed : 19.02 % 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: -1.84 (0.47), residues: 304 helix: -1.09 (0.54), residues: 87 sheet: -0.51 (0.91), residues: 28 loop : -1.43 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 291 HIS 0.002 0.001 HIS q 112 PHE 0.009 0.001 PHE q 235 TYR 0.004 0.001 TYR q 124 ARG 0.004 0.001 ARG q 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1294.38 seconds wall clock time: 23 minutes 40.48 seconds (1420.48 seconds total)