Starting phenix.real_space_refine on Wed Mar 5 15:24:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y14_33556/03_2025/7y14_33556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y14_33556/03_2025/7y14_33556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2025/7y14_33556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2025/7y14_33556.map" model { file = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2025/7y14_33556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2025/7y14_33556.cif" } resolution = 3.2 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= -0.003 sd= 0.055 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 22 5.16 5 C 1431 2.51 5 N 342 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 2145 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2073 Unusual residues: {'BAL': 1} Classifications: {'peptide': 264, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PRE-BETA-TRANS': 1, 'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PLM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.52, per 1000 atoms: 1.17 Number of scatterers: 2145 At special positions: 0 Unit cell: (57.375, 68.175, 69.525, 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 22 16.00 O 350 8.00 N 342 7.00 C 1431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 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: 0.68 Conformation dependent library (CDL) restraints added in 269.3 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 512 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 22 through 52 removed outlier: 3.709A pdb=" N LEU R 28 " --> pdb=" O HIS R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 86 Processing helix chain 'R' and resid 95 through 129 removed outlier: 3.733A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 Processing helix chain 'R' and resid 172 through 189 Processing helix chain 'R' and resid 189 through 209 Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 234 through 242 removed outlier: 4.188A pdb=" N SER R 238 " --> pdb=" O SER R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix 171 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: 0.56 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 427 1.33 - 1.45: 506 1.45 - 1.57: 1230 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 2196 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.566 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CA BAL R1001 " pdb=" C BAL R1001 " ideal model delta sigma weight residual 1.525 1.500 0.025 2.10e-02 2.27e+03 1.40e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.565 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 2836 1.49 - 2.98: 113 2.98 - 4.47: 12 4.47 - 5.96: 5 5.96 - 7.46: 3 Bond angle restraints: 2969 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.34 7.46 1.70e+00 3.46e-01 1.92e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.23e+00 angle pdb=" N MET R 79 " pdb=" CA MET R 79 " pdb=" CB MET R 79 " ideal model delta sigma weight residual 110.16 113.87 -3.71 1.48e+00 4.57e-01 6.30e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 118.12 -4.52 1.90e+00 2.77e-01 5.65e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.15 3.99 1.75e+00 3.27e-01 5.19e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 1146 16.25 - 32.51: 131 32.51 - 48.76: 20 48.76 - 65.01: 3 65.01 - 81.27: 1 Dihedral angle restraints: 1301 sinusoidal: 519 harmonic: 782 Sorted by residual: dihedral pdb=" CB GLU R 99 " pdb=" CG GLU R 99 " pdb=" CD GLU R 99 " pdb=" OE1 GLU R 99 " ideal model delta sinusoidal sigma weight residual 0.00 81.27 -81.27 1 3.00e+01 1.11e-03 9.05e+00 dihedral pdb=" CB MET R 180 " pdb=" CG MET R 180 " pdb=" SD MET R 180 " pdb=" CE MET R 180 " ideal model delta sinusoidal sigma weight residual 60.00 110.60 -50.60 3 1.50e+01 4.44e-03 8.92e+00 dihedral pdb=" CA LEU R 228 " pdb=" CB LEU R 228 " pdb=" CG LEU R 228 " pdb=" CD1 LEU R 228 " ideal model delta sinusoidal sigma weight residual 180.00 134.54 45.46 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 1298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 224 0.031 - 0.063: 95 0.063 - 0.094: 22 0.094 - 0.125: 5 0.125 - 0.157: 5 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA MET R 79 " pdb=" N MET R 79 " pdb=" C MET R 79 " pdb=" CB MET R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA THR R 191 " pdb=" N THR R 191 " pdb=" C THR R 191 " pdb=" CB THR R 191 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 348 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.020 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" CG TRP R 144 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 88 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R 89 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN R 215 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO R 216 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.021 5.00e-02 4.00e+02 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 631 2.83 - 3.35: 2146 3.35 - 3.86: 3635 3.86 - 4.38: 3981 4.38 - 4.90: 7063 Nonbonded interactions: 17456 Sorted by model distance: nonbonded pdb=" OD2 ASP R 179 " pdb=" N BAL R1001 " model vdw 2.312 3.120 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.332 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.460 3.040 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.461 3.120 nonbonded pdb=" O GLY R 41 " pdb=" ND2 ASN R 45 " model vdw 2.471 3.120 ... (remaining 17451 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=0.00 max=1.00 mean=0.99 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.420 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2196 Z= 0.258 Angle : 0.663 7.456 2969 Z= 0.351 Chirality : 0.039 0.157 351 Planarity : 0.005 0.059 348 Dihedral : 13.603 81.268 786 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.39 % 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: 2.46 (0.56), residues: 262 helix: 2.33 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.20 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.022 0.002 PHE R 75 TYR 0.012 0.002 TYR R 106 ARG 0.003 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1020 time to fit residues: 4.7626 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.161871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137173 restraints weight = 2516.537| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.74 r_work: 0.3368 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2196 Z= 0.181 Angle : 0.544 6.551 2969 Z= 0.277 Chirality : 0.037 0.153 351 Planarity : 0.005 0.056 348 Dihedral : 7.554 59.172 342 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.43 % Allowed : 5.19 % Favored : 94.37 % Cbeta Deviations : 0.39 % 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: 2.88 (0.55), residues: 262 helix: 2.62 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.19 (1.01), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.019 0.002 PHE R 75 TYR 0.016 0.002 TYR R 245 ARG 0.002 0.000 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.267 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0971 time to fit residues: 4.1509 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.156917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131530 restraints weight = 2553.837| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.75 r_work: 0.3342 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.190 Angle : 0.535 6.568 2969 Z= 0.271 Chirality : 0.038 0.154 351 Planarity : 0.005 0.053 348 Dihedral : 7.573 59.078 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.30 % Allowed : 8.66 % Favored : 90.04 % Cbeta Deviations : 0.39 % 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: 3.06 (0.56), residues: 262 helix: 2.71 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.09 (1.05), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.016 0.002 PHE R 75 TYR 0.016 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.226 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.1043 time to fit residues: 4.2141 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132500 restraints weight = 2470.583| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.73 r_work: 0.3357 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.162 Angle : 0.505 6.524 2969 Z= 0.257 Chirality : 0.037 0.154 351 Planarity : 0.005 0.050 348 Dihedral : 7.275 58.311 342 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 12.99 % Favored : 86.58 % Cbeta Deviations : 0.39 % 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: 3.29 (0.55), residues: 262 helix: 2.95 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.25 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.015 0.001 PHE R 75 TYR 0.018 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.229 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0986 time to fit residues: 4.3310 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.157208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131345 restraints weight = 2487.251| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.73 r_work: 0.3361 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2196 Z= 0.159 Angle : 0.513 5.614 2969 Z= 0.261 Chirality : 0.036 0.140 351 Planarity : 0.005 0.049 348 Dihedral : 7.225 58.552 342 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.43 % Allowed : 16.88 % Favored : 82.68 % Cbeta Deviations : 0.39 % 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: 3.33 (0.55), residues: 262 helix: 2.99 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.27 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.016 0.001 PHE R 75 TYR 0.018 0.002 TYR R 245 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.211 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0985 time to fit residues: 4.1843 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.157892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132035 restraints weight = 2508.057| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.74 r_work: 0.3354 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.171 Angle : 0.507 5.429 2969 Z= 0.261 Chirality : 0.037 0.143 351 Planarity : 0.005 0.048 348 Dihedral : 7.269 59.392 342 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.73 % Allowed : 16.02 % Favored : 82.25 % Cbeta Deviations : 0.39 % 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: 3.28 (0.55), residues: 262 helix: 2.89 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.18 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.018 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.229 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.0986 time to fit residues: 4.3619 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 12 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 = 0.3815 r_free = 0.3815 target = 0.158049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132227 restraints weight = 2529.422| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.75 r_work: 0.3349 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.179 Angle : 0.515 5.361 2969 Z= 0.265 Chirality : 0.037 0.144 351 Planarity : 0.005 0.047 348 Dihedral : 7.262 58.256 342 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.30 % Allowed : 16.88 % Favored : 81.82 % Cbeta Deviations : 0.39 % 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: 3.24 (0.55), residues: 262 helix: 2.87 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.22 (1.02), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.020 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.228 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1005 time to fit residues: 4.2918 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.0000 chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.158840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132640 restraints weight = 2512.000| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.75 r_work: 0.3374 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2196 Z= 0.146 Angle : 0.521 7.862 2969 Z= 0.263 Chirality : 0.036 0.135 351 Planarity : 0.005 0.047 348 Dihedral : 7.004 57.635 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.87 % Allowed : 19.48 % Favored : 79.65 % Cbeta Deviations : 0.39 % 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: 3.38 (0.55), residues: 262 helix: 3.05 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.39 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 144 HIS 0.001 0.000 HIS R 140 PHE 0.020 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.206 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.0937 time to fit residues: 4.1120 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.0030 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.158590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132586 restraints weight = 2524.241| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.75 r_work: 0.3365 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2196 Z= 0.169 Angle : 0.506 5.314 2969 Z= 0.262 Chirality : 0.037 0.142 351 Planarity : 0.005 0.046 348 Dihedral : 7.123 59.746 342 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.30 % Allowed : 19.48 % Favored : 79.22 % Cbeta Deviations : 0.39 % 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: 3.39 (0.55), residues: 262 helix: 3.05 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.38 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.022 0.001 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.234 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.0989 time to fit residues: 4.2353 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 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 = 0.3797 r_free = 0.3797 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130333 restraints weight = 2515.975| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.73 r_work: 0.3351 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.178 Angle : 0.523 5.266 2969 Z= 0.271 Chirality : 0.037 0.144 351 Planarity : 0.005 0.046 348 Dihedral : 7.197 57.749 342 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.30 % Allowed : 18.61 % Favored : 80.09 % Cbeta Deviations : 0.39 % 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: 3.30 (0.55), residues: 262 helix: 2.98 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.35 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.022 0.001 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.214 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.0958 time to fit residues: 4.0821 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132285 restraints weight = 2510.768| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.74 r_work: 0.3355 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2196 Z= 0.178 Angle : 0.526 5.263 2969 Z= 0.275 Chirality : 0.037 0.143 351 Planarity : 0.005 0.046 348 Dihedral : 7.167 58.152 342 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.30 % Allowed : 19.48 % Favored : 79.22 % Cbeta Deviations : 0.39 % 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: 3.29 (0.55), residues: 262 helix: 2.97 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.35 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.029 0.002 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1612.14 seconds wall clock time: 28 minutes 22.10 seconds (1702.10 seconds total)