Starting phenix.real_space_refine on Wed Mar 5 15:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzq_24774/03_2025/7rzq_24774.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzq_24774/03_2025/7rzq_24774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzq_24774/03_2025/7rzq_24774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzq_24774/03_2025/7rzq_24774.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzq_24774/03_2025/7rzq_24774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzq_24774/03_2025/7rzq_24774.cif" } resolution = 2.09 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= 0.001 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: 3 Type Number sf(0) Gaussians C 1491 2.51 5 N 424 2.21 5 O 506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2421 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 266 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 2.18, per 1000 atoms: 0.90 Number of scatterers: 2421 At special positions: 0 Unit cell: (44.8938, 51.4238, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 506 8.00 N 424 7.00 C 1491 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: 0.64 Conformation dependent library (CDL) restraints added in 309.8 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 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: 0.69 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 461 1.29 - 1.35: 397 1.35 - 1.42: 53 1.42 - 1.48: 358 1.48 - 1.54: 1152 Bond restraints: 2421 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.98e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.29e-01 bond pdb=" CA ASN E1178 " pdb=" CB ASN E1178 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.70e-02 3.46e+03 8.23e-01 bond pdb=" N ILE F1179 " pdb=" CA ILE F1179 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.25e-02 6.40e+03 8.17e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.98e-01 ... (remaining 2416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.67: 3048 0.67 - 1.34: 169 1.34 - 2.00: 35 2.00 - 2.67: 6 2.67 - 3.34: 6 Bond angle restraints: 3264 Sorted by residual: angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 113.20 111.55 1.65 9.60e-01 1.09e+00 2.96e+00 angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 113.20 111.56 1.64 9.60e-01 1.09e+00 2.93e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 113.20 111.57 1.63 9.60e-01 1.09e+00 2.87e+00 angle pdb=" CA ARG A 983 " pdb=" CB ARG A 983 " pdb=" CG ARG A 983 " ideal model delta sigma weight residual 114.10 117.44 -3.34 2.00e+00 2.50e-01 2.79e+00 angle pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " pdb=" CG ARG C 983 " ideal model delta sigma weight residual 114.10 117.39 -3.29 2.00e+00 2.50e-01 2.71e+00 ... (remaining 3259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 1400 16.80 - 33.60: 88 33.60 - 50.40: 15 50.40 - 67.21: 6 67.21 - 84.01: 9 Dihedral angle restraints: 1518 sinusoidal: 588 harmonic: 930 Sorted by residual: dihedral pdb=" CG ARG B 983 " pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sinusoidal sigma weight residual -180.00 -137.17 -42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CG ARG C 983 " pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sinusoidal sigma weight residual 180.00 -137.20 -42.80 2 1.50e+01 4.44e-03 9.85e+00 dihedral pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " ideal model delta sinusoidal sigma weight residual 180.00 -137.21 -42.79 2 1.50e+01 4.44e-03 9.85e+00 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 175 0.021 - 0.043: 156 0.043 - 0.064: 66 0.064 - 0.085: 11 0.085 - 0.106: 6 Chirality restraints: 414 Sorted by residual: chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.74e-01 chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.70e-01 ... (remaining 411 not shown) Planarity restraints: 429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.100 9.50e-02 1.11e+02 4.50e-02 1.49e+00 pdb=" NE ARG B 983 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 983 " 0.099 9.50e-02 1.11e+02 4.47e-02 1.46e+00 pdb=" NE ARG C 983 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 983 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 983 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 983 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.098 9.50e-02 1.11e+02 4.43e-02 1.43e+00 pdb=" NE ARG A 983 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.001 2.00e-02 2.50e+03 ... (remaining 426 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 818 2.85 - 3.36: 2698 3.36 - 3.88: 4086 3.88 - 4.39: 4441 4.39 - 4.90: 7889 Nonbonded interactions: 19932 Sorted by model distance: nonbonded pdb=" O GLY A 971 " pdb=" OG SER A 974 " model vdw 2.339 3.040 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.340 3.040 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.340 3.040 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.354 3.040 nonbonded pdb=" OG SER C 943 " pdb=" OE2 GLU E1182 " model vdw 2.354 3.040 ... (remaining 19927 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1166 through 1200) selection = (chain 'F' and resid 1166 through 1200) } 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: 0.830 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.090 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:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.006 0.035 2421 Z= 0.399 Angle : 0.396 3.339 3264 Z= 0.240 Chirality : 0.034 0.106 414 Planarity : 0.004 0.045 429 Dihedral : 14.232 84.007 904 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 2.15 (0.43), residues: 310 helix: 2.17 (0.28), residues: 246 sheet: None (None), residues: 0 loop : -1.64 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.009 0.002 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.6388 time to fit residues: 16.2689 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 949 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.148511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.131868 restraints weight = 3052.396| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.68 r_work: 0.4015 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2421 Z= 0.200 Angle : 0.317 2.790 3264 Z= 0.184 Chirality : 0.032 0.103 414 Planarity : 0.002 0.014 429 Dihedral : 2.991 9.155 322 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 3.93 % Favored : 95.71 % 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: 4.68 (0.45), residues: 310 helix: 4.01 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -0.83 (0.77), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 970 ARG 0.003 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.321 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.7641 time to fit residues: 16.4447 Evaluate side-chains 19 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.149332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.132244 restraints weight = 3053.655| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 1.66 r_work: 0.4052 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2421 Z= 0.176 Angle : 0.282 2.374 3264 Z= 0.165 Chirality : 0.032 0.108 414 Planarity : 0.001 0.008 429 Dihedral : 2.829 9.611 322 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 4.29 % Favored : 95.36 % 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: 5.55 (0.44), residues: 310 helix: 4.60 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.35 (0.84), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.002 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.294 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.5860 time to fit residues: 13.8267 Evaluate side-chains 23 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.151303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.134284 restraints weight = 2972.836| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.66 r_work: 0.4064 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2421 Z= 0.255 Angle : 0.322 2.703 3264 Z= 0.186 Chirality : 0.033 0.110 414 Planarity : 0.002 0.008 429 Dihedral : 2.964 9.558 322 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 4.29 % Favored : 94.64 % 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: 5.45 (0.44), residues: 310 helix: 4.51 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.28 (0.80), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 927 ARG 0.003 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.323 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.5468 time to fit residues: 14.6681 Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.151239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.134024 restraints weight = 2990.775| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.67 r_work: 0.4068 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2421 Z= 0.203 Angle : 0.289 2.217 3264 Z= 0.169 Chirality : 0.032 0.108 414 Planarity : 0.001 0.006 429 Dihedral : 2.843 9.386 322 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 5.00 % Favored : 93.93 % 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: 5.77 (0.44), residues: 310 helix: 4.74 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.19 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 927 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.279 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.5156 time to fit residues: 13.8201 Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.143107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.124290 restraints weight = 3009.028| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.74 r_work: 0.4055 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2421 Z= 0.203 Angle : 0.292 2.931 3264 Z= 0.172 Chirality : 0.032 0.109 414 Planarity : 0.001 0.010 429 Dihedral : 2.842 9.058 322 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 5.36 % Favored : 93.57 % 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: 5.81 (0.43), residues: 310 helix: 4.74 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.09 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.290 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5452 time to fit residues: 14.0052 Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.143512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.124950 restraints weight = 3029.597| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.74 r_work: 0.4061 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2421 Z= 0.156 Angle : 0.263 2.422 3264 Z= 0.157 Chirality : 0.031 0.107 414 Planarity : 0.001 0.006 429 Dihedral : 2.729 8.960 322 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 5.71 % Favored : 93.21 % 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: 6.11 (0.43), residues: 310 helix: 4.96 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.01 (0.80), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 970 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.258 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.5221 time to fit residues: 14.5522 Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.151350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133965 restraints weight = 3038.185| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.69 r_work: 0.4067 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.195 Angle : 0.288 3.172 3264 Z= 0.172 Chirality : 0.032 0.109 414 Planarity : 0.001 0.006 429 Dihedral : 2.797 10.196 322 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.14 % Favored : 91.79 % 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: 5.68 (0.44), residues: 310 helix: 4.39 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.11 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.307 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5697 time to fit residues: 14.7083 Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133905 restraints weight = 2999.623| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 1.67 r_work: 0.4067 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2421 Z= 0.226 Angle : 0.300 2.523 3264 Z= 0.176 Chirality : 0.033 0.110 414 Planarity : 0.001 0.012 429 Dihedral : 2.869 10.151 322 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.14 % Favored : 91.79 % 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: 5.55 (0.44), residues: 310 helix: 4.30 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.10 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 927 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.294 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.5685 time to fit residues: 13.9993 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.151314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.133980 restraints weight = 3015.768| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.69 r_work: 0.4018 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.196 Angle : 0.288 3.140 3264 Z= 0.172 Chirality : 0.032 0.108 414 Planarity : 0.001 0.008 429 Dihedral : 2.813 10.107 322 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.50 % Favored : 91.43 % 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: 5.67 (0.44), residues: 310 helix: 4.37 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.16 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.001 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.261 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.5542 time to fit residues: 13.5909 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.143247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.124625 restraints weight = 3019.979| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 1.72 r_work: 0.4028 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.195 Angle : 0.283 2.542 3264 Z= 0.167 Chirality : 0.032 0.109 414 Planarity : 0.001 0.006 429 Dihedral : 2.808 10.063 322 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 7.86 % Favored : 91.43 % 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: 5.67 (0.44), residues: 310 helix: 4.38 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.14 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.001 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.01 seconds wall clock time: 44 minutes 27.10 seconds (2667.10 seconds total)