Starting phenix.real_space_refine on Wed Jul 23 07:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8acb_15345/07_2025/8acb_15345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8acb_15345/07_2025/8acb_15345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2025/8acb_15345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2025/8acb_15345.map" model { file = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2025/8acb_15345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8acb_15345/07_2025/8acb_15345.cif" } resolution = 2.6 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= 0.002 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 11 5.16 5 C 1116 2.51 5 N 314 2.21 5 O 369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 1815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1715 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 2.25, per 1000 atoms: 1.24 Number of scatterers: 1815 At special positions: 0 Unit cell: (79.875, 75.615, 123.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 5 15.00 O 369 8.00 N 314 7.00 C 1116 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: 0.46 Conformation dependent library (CDL) restraints added in 245.4 milliseconds 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 412 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 47.3% alpha, 4.5% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.856A pdb=" N THR A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.581A pdb=" N VAL A 127 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 128 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.629A pdb=" N ILE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 4.197A pdb=" N HIS A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.571A pdb=" N ILE A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.550A pdb=" N GLU A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 240 through 244 removed outlier: 4.417A pdb=" N ARG A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.581A pdb=" N ALA A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.607A pdb=" N GLU A 186 " --> pdb=" O ASP A 183 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.48 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 594 1.34 - 1.46: 308 1.46 - 1.57: 928 1.57 - 1.69: 9 1.69 - 1.81: 21 Bond restraints: 1860 Sorted by residual: bond pdb=" O5' U B 2 " pdb=" C5' U B 2 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.06e+00 bond pdb=" O5' U B 5 " pdb=" C5' U B 5 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.77e+00 bond pdb=" P U B 4 " pdb=" O5' U B 4 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.50e-02 4.44e+03 3.57e+00 bond pdb=" O5' U B 1 " pdb=" C5' U B 1 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.25e+00 bond pdb=" O5' U B 3 " pdb=" C5' U B 3 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.14e+00 ... (remaining 1855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 2487 2.05 - 4.11: 38 4.11 - 6.16: 15 6.16 - 8.21: 3 8.21 - 10.27: 1 Bond angle restraints: 2544 Sorted by residual: angle pdb=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 120.20 109.93 10.27 1.50e+00 4.44e-01 4.68e+01 angle pdb=" O4' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " ideal model delta sigma weight residual 106.10 101.15 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" C2' U B 4 " ideal model delta sigma weight residual 102.60 98.80 3.80 1.00e+00 1.00e+00 1.45e+01 angle pdb=" C3' U B 2 " pdb=" O3' U B 2 " pdb=" P U B 3 " ideal model delta sigma weight residual 120.20 114.83 5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" O3' U B 4 " pdb=" P U B 5 " pdb=" O5' U B 5 " ideal model delta sigma weight residual 104.00 108.21 -4.21 1.50e+00 4.44e-01 7.89e+00 ... (remaining 2539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 1093 33.02 - 66.03: 30 66.03 - 99.05: 1 99.05 - 132.06: 0 132.06 - 165.08: 1 Dihedral angle restraints: 1125 sinusoidal: 485 harmonic: 640 Sorted by residual: dihedral pdb=" O4' U B 5 " pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sinusoidal sigma weight residual 200.00 34.92 165.08 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" C5' U B 4 " pdb=" C4' U B 4 " pdb=" C3' U B 4 " pdb=" O3' U B 4 " ideal model delta sinusoidal sigma weight residual 147.00 179.12 -32.12 1 8.00e+00 1.56e-02 2.30e+01 dihedral pdb=" C3' U B 4 " pdb=" C4' U B 4 " pdb=" O4' U B 4 " pdb=" C1' U B 4 " ideal model delta sinusoidal sigma weight residual -2.00 -34.08 32.08 1 8.00e+00 1.56e-02 2.29e+01 ... (remaining 1122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 273 0.112 - 0.223: 6 0.223 - 0.335: 1 0.335 - 0.446: 1 0.446 - 0.558: 4 Chirality restraints: 285 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" P U B 4 " pdb=" OP1 U B 4 " pdb=" OP2 U B 4 " pdb=" O5' U B 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.44e+00 ... (remaining 282 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 103 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 104 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU A 282 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 282 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP A 283 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 121 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO A 122 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " 0.012 5.00e-02 4.00e+02 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 420 2.79 - 3.31: 1676 3.31 - 3.84: 2816 3.84 - 4.37: 3266 4.37 - 4.90: 5307 Nonbonded interactions: 13485 Sorted by model distance: nonbonded pdb=" OD1 ASP A 239 " pdb=" OG SER A 241 " model vdw 2.257 3.040 nonbonded pdb=" O GLY A 156 " pdb=" ND2 ASN A 160 " model vdw 2.286 3.120 nonbonded pdb=" O PRO A 257 " pdb=" NZ LYS A 261 " model vdw 2.291 3.120 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR A 227 " model vdw 2.319 3.040 nonbonded pdb=" NE2 GLN A 205 " pdb=" OP1 U B 2 " model vdw 2.485 3.120 ... (remaining 13480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 0.570 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.040 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.004 0.035 1860 Z= 0.196 Angle : 0.711 10.266 2544 Z= 0.384 Chirality : 0.079 0.558 285 Planarity : 0.003 0.025 321 Dihedral : 15.238 165.075 713 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.58), residues: 218 helix: 0.34 (0.55), residues: 89 sheet: 1.47 (1.02), residues: 10 loop : -1.44 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 249 TYR 0.009 0.001 TYR A 245 ARG 0.002 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.23270 ( 61) hydrogen bonds : angle 6.03122 ( 177) covalent geometry : bond 0.00363 ( 1860) covalent geometry : angle 0.71054 ( 2544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.182 Fit side-chains REVERT: A 93 ARG cc_start: 0.5590 (mtt180) cc_final: 0.4671 (mtt180) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.4128 time to fit residues: 81.6437 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 overall best weight: 2.1664 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.147431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126571 restraints weight = 2349.239| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.81 r_work: 0.3333 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1860 Z= 0.123 Angle : 0.551 5.322 2544 Z= 0.276 Chirality : 0.039 0.148 285 Planarity : 0.004 0.035 321 Dihedral : 14.748 170.508 318 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.14 % Allowed : 11.93 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.57), residues: 218 helix: 0.38 (0.53), residues: 96 sheet: 1.38 (1.09), residues: 10 loop : -1.68 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 249 TYR 0.007 0.001 TYR A 245 ARG 0.002 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 61) hydrogen bonds : angle 4.10378 ( 177) covalent geometry : bond 0.00283 ( 1860) covalent geometry : angle 0.55074 ( 2544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.208 Fit side-chains REVERT: A 93 ARG cc_start: 0.5853 (mtt180) cc_final: 0.4653 (mtt180) REVERT: A 138 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: A 186 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7552 (pt0) outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 1.5790 time to fit residues: 84.8259 Evaluate side-chains 51 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 186 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123485 restraints weight = 2398.121| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.81 r_work: 0.3288 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1860 Z= 0.109 Angle : 0.507 4.886 2544 Z= 0.253 Chirality : 0.038 0.130 285 Planarity : 0.003 0.033 321 Dihedral : 14.536 168.997 318 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.27 % Allowed : 14.20 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.57), residues: 218 helix: 0.62 (0.53), residues: 96 sheet: 1.36 (1.25), residues: 10 loop : -1.73 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.010 0.001 PHE A 249 TYR 0.009 0.001 TYR A 190 ARG 0.002 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 61) hydrogen bonds : angle 3.75911 ( 177) covalent geometry : bond 0.00253 ( 1860) covalent geometry : angle 0.50664 ( 2544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.185 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 1.5142 time to fit residues: 79.8085 Evaluate side-chains 48 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.0040 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7652 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.146981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126102 restraints weight = 2406.022| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.86 r_work: 0.3336 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1860 Z= 0.085 Angle : 0.461 4.982 2544 Z= 0.230 Chirality : 0.036 0.110 285 Planarity : 0.003 0.029 321 Dihedral : 14.374 165.992 318 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.70 % Allowed : 16.48 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.58), residues: 218 helix: 0.80 (0.54), residues: 96 sheet: 1.75 (1.36), residues: 10 loop : -1.64 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 249 TYR 0.011 0.001 TYR A 190 ARG 0.001 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 61) hydrogen bonds : angle 3.55082 ( 177) covalent geometry : bond 0.00194 ( 1860) covalent geometry : angle 0.46132 ( 2544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.198 Fit side-chains REVERT: A 93 ARG cc_start: 0.4579 (mtt180) cc_final: 0.3538 (mtm180) REVERT: A 126 GLU cc_start: 0.8663 (mt-10) cc_final: 0.7353 (tm-30) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 1.5661 time to fit residues: 84.1301 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117026 restraints weight = 2333.742| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.79 r_work: 0.3194 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1860 Z= 0.190 Angle : 0.617 7.006 2544 Z= 0.308 Chirality : 0.043 0.154 285 Planarity : 0.005 0.039 321 Dihedral : 14.940 179.138 318 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.84 % Allowed : 17.05 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.58), residues: 218 helix: 0.74 (0.54), residues: 98 sheet: 1.76 (1.42), residues: 10 loop : -1.82 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.002 0.001 HIS A 209 PHE 0.013 0.002 PHE A 249 TYR 0.009 0.002 TYR A 190 ARG 0.003 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 61) hydrogen bonds : angle 3.82114 ( 177) covalent geometry : bond 0.00444 ( 1860) covalent geometry : angle 0.61674 ( 2544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.226 Fit side-chains REVERT: A 93 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.3932 (mtt180) REVERT: A 126 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7376 (tm-30) REVERT: A 138 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: A 219 GLU cc_start: 0.8187 (pt0) cc_final: 0.7971 (pp20) REVERT: A 276 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7257 (ttp-170) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 1.6304 time to fit residues: 84.3100 Evaluate side-chains 51 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.138765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118045 restraints weight = 2421.570| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.83 r_work: 0.3221 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.136 Angle : 0.558 6.174 2544 Z= 0.278 Chirality : 0.040 0.143 285 Planarity : 0.004 0.037 321 Dihedral : 14.739 175.781 318 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.84 % Allowed : 16.48 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.58), residues: 218 helix: 0.82 (0.54), residues: 96 sheet: 2.02 (1.40), residues: 10 loop : -1.78 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 PHE 0.011 0.001 PHE A 249 TYR 0.010 0.001 TYR A 190 ARG 0.002 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 61) hydrogen bonds : angle 3.58350 ( 177) covalent geometry : bond 0.00312 ( 1860) covalent geometry : angle 0.55796 ( 2544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.220 Fit side-chains REVERT: A 93 ARG cc_start: 0.4727 (OUTLIER) cc_final: 0.3692 (mtt180) REVERT: A 126 GLU cc_start: 0.8708 (mt-10) cc_final: 0.7375 (tm-30) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 1.6189 time to fit residues: 90.1853 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.136372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115821 restraints weight = 2340.972| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.78 r_work: 0.3204 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1860 Z= 0.170 Angle : 0.610 7.201 2544 Z= 0.305 Chirality : 0.042 0.156 285 Planarity : 0.005 0.039 321 Dihedral : 14.901 178.054 318 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.27 % Allowed : 17.05 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.58), residues: 218 helix: 0.74 (0.54), residues: 97 sheet: 1.92 (1.43), residues: 10 loop : -1.70 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.004 0.001 HIS A 198 PHE 0.012 0.002 PHE A 249 TYR 0.012 0.002 TYR A 190 ARG 0.002 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 61) hydrogen bonds : angle 3.71370 ( 177) covalent geometry : bond 0.00389 ( 1860) covalent geometry : angle 0.61044 ( 2544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.207 Fit side-chains REVERT: A 93 ARG cc_start: 0.4724 (OUTLIER) cc_final: 0.3753 (mtt180) REVERT: A 126 GLU cc_start: 0.8691 (mt-10) cc_final: 0.7357 (tm-30) REVERT: A 138 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8159 (tm-30) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 1.5000 time to fit residues: 77.5476 Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118464 restraints weight = 2409.866| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.78 r_work: 0.3240 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1860 Z= 0.117 Angle : 0.546 5.645 2544 Z= 0.272 Chirality : 0.039 0.134 285 Planarity : 0.004 0.036 321 Dihedral : 14.777 175.822 318 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.70 % Allowed : 18.18 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.58), residues: 218 helix: 0.82 (0.55), residues: 96 sheet: 1.94 (1.49), residues: 10 loop : -1.76 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 PHE 0.010 0.001 PHE A 249 TYR 0.014 0.002 TYR A 190 ARG 0.002 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 61) hydrogen bonds : angle 3.59423 ( 177) covalent geometry : bond 0.00265 ( 1860) covalent geometry : angle 0.54603 ( 2544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.188 Fit side-chains REVERT: A 93 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.3611 (mtt180) REVERT: A 126 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7431 (tm-30) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 1.6531 time to fit residues: 87.0339 Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117898 restraints weight = 2396.170| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.77 r_work: 0.3233 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1860 Z= 0.129 Angle : 0.559 6.430 2544 Z= 0.276 Chirality : 0.040 0.140 285 Planarity : 0.004 0.036 321 Dihedral : 14.796 176.511 318 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.84 % Allowed : 17.61 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.58), residues: 218 helix: 0.78 (0.54), residues: 96 sheet: 1.84 (1.54), residues: 10 loop : -1.75 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 PHE 0.011 0.001 PHE A 249 TYR 0.015 0.001 TYR A 190 ARG 0.001 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 61) hydrogen bonds : angle 3.60706 ( 177) covalent geometry : bond 0.00294 ( 1860) covalent geometry : angle 0.55896 ( 2544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.187 Fit side-chains REVERT: A 93 ARG cc_start: 0.4725 (OUTLIER) cc_final: 0.3650 (mtt180) REVERT: A 126 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7377 (tm-30) REVERT: A 138 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8128 (tm-30) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 1.6159 time to fit residues: 85.2041 Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 6 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122283 restraints weight = 2464.697| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.84 r_work: 0.3285 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1860 Z= 0.092 Angle : 0.481 5.066 2544 Z= 0.242 Chirality : 0.037 0.112 285 Planarity : 0.004 0.034 321 Dihedral : 14.605 172.055 318 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.14 % Allowed : 19.32 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.58), residues: 218 helix: 0.89 (0.54), residues: 96 sheet: 2.02 (1.55), residues: 10 loop : -1.68 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.002 0.001 HIS A 198 PHE 0.009 0.001 PHE A 249 TYR 0.014 0.001 TYR A 190 ARG 0.002 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 61) hydrogen bonds : angle 3.45861 ( 177) covalent geometry : bond 0.00206 ( 1860) covalent geometry : angle 0.48083 ( 2544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 436 Ramachandran restraints generated. 218 Oldfield, 0 Emsley, 218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.184 Fit side-chains REVERT: A 93 ARG cc_start: 0.4664 (mtt180) cc_final: 0.3648 (mtt180) REVERT: A 126 GLU cc_start: 0.8701 (mt-10) cc_final: 0.7396 (tm-30) REVERT: A 276 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7217 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.5419 time to fit residues: 82.7832 Evaluate side-chains 52 residues out of total 189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 0.0070 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117820 restraints weight = 2358.810| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.75 r_work: 0.3224 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1860 Z= 0.145 Angle : 0.561 6.331 2544 Z= 0.280 Chirality : 0.040 0.138 285 Planarity : 0.004 0.036 321 Dihedral : 14.816 176.972 318 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.14 % Allowed : 19.32 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.58), residues: 218 helix: 0.81 (0.54), residues: 97 sheet: 2.05 (1.57), residues: 10 loop : -1.66 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.003 0.001 HIS A 198 PHE 0.012 0.002 PHE A 249 TYR 0.013 0.002 TYR A 190 ARG 0.002 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 61) hydrogen bonds : angle 3.54826 ( 177) covalent geometry : bond 0.00336 ( 1860) covalent geometry : angle 0.56144 ( 2544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.38 seconds wall clock time: 50 minutes 47.54 seconds (3047.54 seconds total)