Starting phenix.real_space_refine on Tue Feb 3 12:38:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ls1_63350/02_2026/9ls1_63350.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ls1_63350/02_2026/9ls1_63350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ls1_63350/02_2026/9ls1_63350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ls1_63350/02_2026/9ls1_63350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ls1_63350/02_2026/9ls1_63350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ls1_63350/02_2026/9ls1_63350.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 13 5.16 5 C 1324 2.51 5 N 405 2.21 5 O 430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Time building chain proxies: 0.70, per 1000 atoms: 0.32 Number of scatterers: 2172 At special positions: 0 Unit cell: (73.45, 45.2, 152.55, 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 13 16.00 O 430 8.00 N 405 7.00 C 1324 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: 0.18 Conformation dependent library (CDL) restraints added in 85.6 milliseconds 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 526 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 2 sheets defined 72.9% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 42 through 98 removed outlier: 4.015A pdb=" N GLU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.645A pdb=" N GLU A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 242 removed outlier: 3.504A pdb=" N ILE A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 271 removed outlier: 3.589A pdb=" N VAL A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.538A pdb=" N SER A 278 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 4.209A pdb=" N MET A 149 " --> pdb=" O VAL A 163 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 513 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: 0.20 Time building geometry restraints manager: 0.24 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: 775 1.34 - 1.45: 182 1.45 - 1.57: 1208 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 2191 Sorted by residual: bond pdb=" N ASN A 217 " pdb=" CA ASN A 217 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.33e+00 bond pdb=" N ASN A 211 " pdb=" CA ASN A 211 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.03e+00 bond pdb=" N TYR A 215 " pdb=" CA TYR A 215 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.71e+00 bond pdb=" N LEU A 212 " pdb=" CA LEU A 212 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.39e+00 bond pdb=" N PHE A 216 " pdb=" CA PHE A 216 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.94e+00 ... (remaining 2186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 2741 1.00 - 2.01: 169 2.01 - 3.01: 28 3.01 - 4.01: 4 4.01 - 5.01: 2 Bond angle restraints: 2944 Sorted by residual: angle pdb=" CA GLY A 213 " pdb=" C GLY A 213 " pdb=" O GLY A 213 " ideal model delta sigma weight residual 120.75 117.94 2.81 1.03e+00 9.43e-01 7.46e+00 angle pdb=" CA ASN A 217 " pdb=" C ASN A 217 " pdb=" O ASN A 217 " ideal model delta sigma weight residual 120.82 118.03 2.79 1.05e+00 9.07e-01 7.08e+00 angle pdb=" CA LEU A 212 " pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 120.55 117.84 2.71 1.06e+00 8.90e-01 6.52e+00 angle pdb=" CA ASN A 211 " pdb=" C ASN A 211 " pdb=" O ASN A 211 " ideal model delta sigma weight residual 120.82 118.19 2.63 1.05e+00 9.07e-01 6.26e+00 angle pdb=" O GLY A 213 " pdb=" C GLY A 213 " pdb=" N ALA A 214 " ideal model delta sigma weight residual 122.19 124.50 -2.31 9.60e-01 1.09e+00 5.78e+00 ... (remaining 2939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1149 17.70 - 35.40: 142 35.40 - 53.10: 55 53.10 - 70.80: 10 70.80 - 88.50: 6 Dihedral angle restraints: 1362 sinusoidal: 554 harmonic: 808 Sorted by residual: dihedral pdb=" CA ASN A 156 " pdb=" C ASN A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N LEU A 183 " pdb=" CA LEU A 183 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CG ARG A 53 " pdb=" CD ARG A 53 " pdb=" NE ARG A 53 " pdb=" CZ ARG A 53 " ideal model delta sinusoidal sigma weight residual -90.00 -134.50 44.50 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 1359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 158 0.025 - 0.050: 113 0.050 - 0.075: 42 0.075 - 0.100: 14 0.100 - 0.125: 9 Chirality restraints: 336 Sorted by residual: chirality pdb=" CA PHE A 18 " pdb=" N PHE A 18 " pdb=" C PHE A 18 " pdb=" CB PHE A 18 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 333 not shown) Planarity restraints: 393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 18 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C PHE A 18 " 0.024 2.00e-02 2.50e+03 pdb=" O PHE A 18 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN A 19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 18 " -0.013 2.00e-02 2.50e+03 9.72e-03 1.65e+00 pdb=" CG PHE A 18 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 18 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 18 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 154 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 155 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " 0.014 5.00e-02 4.00e+02 ... (remaining 390 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 423 2.78 - 3.31: 2119 3.31 - 3.84: 3759 3.84 - 4.37: 3999 4.37 - 4.90: 6860 Nonbonded interactions: 17160 Sorted by model distance: nonbonded pdb=" N GLU A 104 " pdb=" OE1 GLU A 104 " model vdw 2.252 3.120 nonbonded pdb=" ND2 ASN A 26 " pdb=" OE2 GLU A 248 " model vdw 2.303 3.120 nonbonded pdb=" O THR A 187 " pdb=" OG SER A 191 " model vdw 2.358 3.040 nonbonded pdb=" O ALA A 246 " pdb=" OG1 THR A 249 " model vdw 2.390 3.040 nonbonded pdb=" OG SER A 49 " pdb=" OE2 GLU A 237 " model vdw 2.424 3.040 ... (remaining 17155 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 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: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.190 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.005 0.030 2191 Z= 0.246 Angle : 0.547 5.013 2944 Z= 0.345 Chirality : 0.040 0.125 336 Planarity : 0.004 0.025 393 Dihedral : 19.232 88.504 836 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.14 % Allowed : 23.93 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.47), residues: 278 helix: 3.41 (0.33), residues: 196 sheet: None (None), residues: 0 loop : -1.36 (0.56), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.008 0.002 TYR A 230 PHE 0.022 0.002 PHE A 18 TRP 0.004 0.001 TRP A 150 HIS 0.005 0.002 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 2191) covalent geometry : angle 0.54729 ( 2944) hydrogen bonds : bond 0.11903 ( 178) hydrogen bonds : angle 3.77081 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.083 Fit side-chains REVERT: A 19 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7840 (tp-100) REVERT: A 239 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8170 (mtm-85) REVERT: A 268 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8566 (mt0) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.7713 time to fit residues: 42.1901 Evaluate side-chains 59 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 268 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.125943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113288 restraints weight = 2287.519| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.96 r_work: 0.3147 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2191 Z= 0.160 Angle : 0.448 4.600 2944 Z= 0.258 Chirality : 0.036 0.116 336 Planarity : 0.003 0.022 393 Dihedral : 7.175 58.975 315 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.14 % Allowed : 24.36 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.48), residues: 278 helix: 3.78 (0.33), residues: 198 sheet: None (None), residues: 0 loop : -1.22 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.006 0.001 TYR A 215 PHE 0.015 0.002 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2191) covalent geometry : angle 0.44817 ( 2944) hydrogen bonds : bond 0.07184 ( 178) hydrogen bonds : angle 3.37220 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.054 Fit side-chains REVERT: A 119 ASP cc_start: 0.8234 (t0) cc_final: 0.8023 (t70) REVERT: A 239 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8204 (mtt90) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.7889 time to fit residues: 43.9333 Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 265 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.127203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114912 restraints weight = 2267.549| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 0.93 r_work: 0.3147 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2191 Z= 0.163 Angle : 0.449 4.654 2944 Z= 0.259 Chirality : 0.036 0.114 336 Planarity : 0.003 0.032 393 Dihedral : 4.635 32.718 305 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.99 % Allowed : 23.93 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.48), residues: 278 helix: 3.81 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.17 (0.59), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.005 0.001 TYR A 215 PHE 0.016 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2191) covalent geometry : angle 0.44904 ( 2944) hydrogen bonds : bond 0.07237 ( 178) hydrogen bonds : angle 3.36910 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.091 Fit side-chains REVERT: A 19 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7906 (tp-100) REVERT: A 35 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8333 (ttt-90) REVERT: A 119 ASP cc_start: 0.8245 (t0) cc_final: 0.8027 (t70) REVERT: A 181 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: A 239 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8201 (mtm-85) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.8545 time to fit residues: 49.3630 Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.127008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114593 restraints weight = 2270.791| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.94 r_work: 0.3219 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2191 Z= 0.149 Angle : 0.429 4.487 2944 Z= 0.248 Chirality : 0.035 0.114 336 Planarity : 0.003 0.024 393 Dihedral : 4.516 31.418 305 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.70 % Allowed : 22.65 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.48), residues: 278 helix: 3.93 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.15 (0.59), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.005 0.001 TYR A 215 PHE 0.014 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2191) covalent geometry : angle 0.42903 ( 2944) hydrogen bonds : bond 0.06843 ( 178) hydrogen bonds : angle 3.30630 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.093 Fit side-chains REVERT: A 35 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8329 (ttt-90) REVERT: A 119 ASP cc_start: 0.8225 (t0) cc_final: 0.8016 (t70) REVERT: A 181 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: A 239 ARG cc_start: 0.8459 (mtm180) cc_final: 0.8185 (mtm-85) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.8805 time to fit residues: 49.9609 Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.126764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114177 restraints weight = 2277.055| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.00 r_work: 0.3109 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2191 Z= 0.219 Angle : 0.518 5.080 2944 Z= 0.296 Chirality : 0.040 0.127 336 Planarity : 0.004 0.037 393 Dihedral : 4.869 35.251 305 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.70 % Allowed : 22.65 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.47), residues: 278 helix: 3.46 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.19 (0.59), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 35 TYR 0.003 0.001 TYR A 230 PHE 0.022 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.006 0.002 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 2191) covalent geometry : angle 0.51779 ( 2944) hydrogen bonds : bond 0.08166 ( 178) hydrogen bonds : angle 3.54273 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.103 Fit side-chains REVERT: A 19 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7926 (tp-100) REVERT: A 35 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8339 (ttt-90) REVERT: A 181 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: A 239 ARG cc_start: 0.8498 (mtm180) cc_final: 0.8216 (mtt90) outliers start: 11 outliers final: 4 residues processed: 57 average time/residue: 0.7637 time to fit residues: 44.1187 Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 268 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 21 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.130889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118512 restraints weight = 2284.164| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.00 r_work: 0.3204 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2191 Z= 0.130 Angle : 0.408 4.431 2944 Z= 0.236 Chirality : 0.034 0.115 336 Planarity : 0.002 0.021 393 Dihedral : 4.367 29.617 305 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.85 % Allowed : 23.08 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.49), residues: 278 helix: 4.09 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.18 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.005 0.001 TYR A 215 PHE 0.010 0.001 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2191) covalent geometry : angle 0.40790 ( 2944) hydrogen bonds : bond 0.06222 ( 178) hydrogen bonds : angle 3.21088 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.115 Fit side-chains REVERT: A 19 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7878 (tp-100) REVERT: A 35 ARG cc_start: 0.8568 (ttp80) cc_final: 0.8318 (ttt-90) REVERT: A 239 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8168 (mtm-85) outliers start: 9 outliers final: 3 residues processed: 56 average time/residue: 0.7512 time to fit residues: 42.6379 Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 139 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116632 restraints weight = 2308.634| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.00 r_work: 0.3179 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2191 Z= 0.160 Angle : 0.456 5.087 2944 Z= 0.260 Chirality : 0.036 0.114 336 Planarity : 0.003 0.024 393 Dihedral : 4.548 31.026 305 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.27 % Allowed : 23.08 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.90 (0.48), residues: 278 helix: 3.91 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.16 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.004 0.001 TYR A 215 PHE 0.015 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2191) covalent geometry : angle 0.45613 ( 2944) hydrogen bonds : bond 0.07069 ( 178) hydrogen bonds : angle 3.33614 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.054 Fit side-chains REVERT: A 19 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7889 (tp-100) REVERT: A 35 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8348 (ttt-90) REVERT: A 160 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8443 (ptm-80) REVERT: A 181 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6761 (pm20) REVERT: A 193 ASP cc_start: 0.8394 (m-30) cc_final: 0.8114 (m-30) REVERT: A 239 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8162 (mtt90) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.6764 time to fit residues: 39.0753 Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 181 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 15 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 overall best weight: 0.2436 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.130004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117861 restraints weight = 2280.416| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.94 r_work: 0.3199 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2191 Z= 0.129 Angle : 0.403 4.343 2944 Z= 0.232 Chirality : 0.034 0.115 336 Planarity : 0.002 0.020 393 Dihedral : 4.283 27.697 305 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.56 % Allowed : 23.93 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.22 (0.49), residues: 278 helix: 4.19 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.18 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.005 0.001 TYR A 215 PHE 0.010 0.001 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 2191) covalent geometry : angle 0.40292 ( 2944) hydrogen bonds : bond 0.06146 ( 178) hydrogen bonds : angle 3.18872 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.055 Fit side-chains REVERT: A 19 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7863 (tp-100) REVERT: A 35 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8336 (ttt-90) REVERT: A 160 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8426 (ptm-80) REVERT: A 239 ARG cc_start: 0.8424 (mtm180) cc_final: 0.8159 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.5156 time to fit residues: 27.7507 Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.127870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.115194 restraints weight = 2299.677| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.01 r_work: 0.3186 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2191 Z= 0.180 Angle : 0.475 4.818 2944 Z= 0.271 Chirality : 0.037 0.113 336 Planarity : 0.003 0.027 393 Dihedral : 4.633 31.573 305 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.42 % Allowed : 23.50 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.48), residues: 278 helix: 3.84 (0.33), residues: 196 sheet: None (None), residues: 0 loop : -1.17 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.004 0.001 TYR A 230 PHE 0.019 0.002 PHE A 18 TRP 0.001 0.001 TRP A 150 HIS 0.005 0.002 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2191) covalent geometry : angle 0.47519 ( 2944) hydrogen bonds : bond 0.07538 ( 178) hydrogen bonds : angle 3.41963 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.054 Fit side-chains REVERT: A 19 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7900 (tp-100) REVERT: A 35 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8363 (ttt-90) REVERT: A 181 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: A 193 ASP cc_start: 0.8415 (m-30) cc_final: 0.8159 (m-30) REVERT: A 239 ARG cc_start: 0.8484 (mtm180) cc_final: 0.8182 (mtt90) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.5488 time to fit residues: 30.5974 Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 268 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.126474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113893 restraints weight = 2322.697| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.96 r_work: 0.3154 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2191 Z= 0.152 Angle : 0.438 4.529 2944 Z= 0.251 Chirality : 0.035 0.113 336 Planarity : 0.003 0.020 393 Dihedral : 4.506 30.512 305 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.85 % Allowed : 23.08 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.49), residues: 278 helix: 3.96 (0.33), residues: 198 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.003 0.001 TYR A 215 PHE 0.014 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2191) covalent geometry : angle 0.43750 ( 2944) hydrogen bonds : bond 0.06915 ( 178) hydrogen bonds : angle 3.31383 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.056 Fit side-chains REVERT: A 19 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7894 (tp-100) REVERT: A 35 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8342 (ttt-90) REVERT: A 160 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8439 (ptm-80) REVERT: A 193 ASP cc_start: 0.8394 (m-30) cc_final: 0.8128 (m-30) REVERT: A 239 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8142 (mtt90) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.5932 time to fit residues: 34.2612 Evaluate side-chains 59 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 268 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.128833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116404 restraints weight = 2347.900| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.97 r_work: 0.3149 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2191 Z= 0.155 Angle : 0.452 6.129 2944 Z= 0.255 Chirality : 0.036 0.114 336 Planarity : 0.003 0.022 393 Dihedral : 4.521 30.680 305 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.42 % Allowed : 23.93 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.49), residues: 278 helix: 3.94 (0.32), residues: 198 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.004 0.001 TYR A 215 PHE 0.015 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2191) covalent geometry : angle 0.45233 ( 2944) hydrogen bonds : bond 0.06978 ( 178) hydrogen bonds : angle 3.32770 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.84 seconds wall clock time: 23 minutes 7.48 seconds (1387.48 seconds total)