Starting phenix.real_space_refine on Wed Mar 5 14:36:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az1_15729/03_2025/8az1_15729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az1_15729/03_2025/8az1_15729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8az1_15729/03_2025/8az1_15729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az1_15729/03_2025/8az1_15729.map" model { file = "/net/cci-nas-00/data/ceres_data/8az1_15729/03_2025/8az1_15729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az1_15729/03_2025/8az1_15729.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1130 2.51 5 N 330 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 1830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 0.83, per 1000 atoms: 0.45 Number of scatterers: 1830 At special positions: 0 Unit cell: (38.64, 86.52, 38.64, 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 370 8.00 N 330 7.00 C 1130 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 240.7 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.460A pdb=" N ASN A 22 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 22 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN E 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN G 22 " --> pdb=" O PHE I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 8.551A pdb=" N THR A 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR C 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR E 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR G 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.442A pdb=" N ASN B 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN F 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN H 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 8.566A pdb=" N THR B 30 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR D 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR F 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR H 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 36 56 hydrogen bonds defined for protein. 168 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: 0.50 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 300 1.29 - 1.35: 311 1.35 - 1.41: 228 1.41 - 1.48: 301 1.48 - 1.54: 710 Bond restraints: 1850 Sorted by residual: bond pdb=" C GLY H 33 " pdb=" O GLY H 33 " ideal model delta sigma weight residual 1.238 1.231 0.006 1.12e-02 7.97e+03 3.34e-01 bond pdb=" C GLY A 20 " pdb=" O GLY A 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 3.07e-01 bond pdb=" C GLY E 20 " pdb=" O GLY E 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 3.04e-01 bond pdb=" C GLY J 33 " pdb=" O GLY J 33 " ideal model delta sigma weight residual 1.238 1.231 0.006 1.12e-02 7.97e+03 2.93e-01 bond pdb=" C GLY I 20 " pdb=" O GLY I 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 2.85e-01 ... (remaining 1845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 2341 0.85 - 1.70: 124 1.70 - 2.55: 25 2.55 - 3.40: 0 3.40 - 4.25: 20 Bond angle restraints: 2510 Sorted by residual: angle pdb=" N GLY B 20 " pdb=" CA GLY B 20 " pdb=" C GLY B 20 " ideal model delta sigma weight residual 113.48 117.73 -4.25 1.46e+00 4.69e-01 8.49e+00 angle pdb=" N GLY I 20 " pdb=" CA GLY I 20 " pdb=" C GLY I 20 " ideal model delta sigma weight residual 113.48 117.71 -4.23 1.46e+00 4.69e-01 8.38e+00 angle pdb=" N GLY D 20 " pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 113.48 117.70 -4.22 1.46e+00 4.69e-01 8.35e+00 angle pdb=" N GLY C 20 " pdb=" CA GLY C 20 " pdb=" C GLY C 20 " ideal model delta sigma weight residual 113.48 117.67 -4.19 1.46e+00 4.69e-01 8.24e+00 angle pdb=" N GLY A 20 " pdb=" CA GLY A 20 " pdb=" C GLY A 20 " ideal model delta sigma weight residual 113.48 117.65 -4.17 1.46e+00 4.69e-01 8.17e+00 ... (remaining 2505 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 7.64: 820 7.64 - 15.28: 110 15.28 - 22.91: 40 22.91 - 30.55: 30 30.55 - 38.18: 10 Dihedral angle restraints: 1010 sinusoidal: 320 harmonic: 690 Sorted by residual: dihedral pdb=" N HIS A 18 " pdb=" CA HIS A 18 " pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.82 -38.18 3 1.50e+01 4.44e-03 6.71e+00 dihedral pdb=" N HIS G 18 " pdb=" CA HIS G 18 " pdb=" CB HIS G 18 " pdb=" CG HIS G 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.89 -38.11 3 1.50e+01 4.44e-03 6.69e+00 dihedral pdb=" N HIS C 18 " pdb=" CA HIS C 18 " pdb=" CB HIS C 18 " pdb=" CG HIS C 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.89 -38.11 3 1.50e+01 4.44e-03 6.69e+00 ... (remaining 1007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 160 0.024 - 0.047: 74 0.047 - 0.071: 26 0.071 - 0.094: 15 0.094 - 0.118: 15 Chirality restraints: 290 Sorted by residual: chirality pdb=" CA ILE E 26 " pdb=" N ILE E 26 " pdb=" C ILE E 26 " pdb=" CB ILE E 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE J 26 " pdb=" N ILE J 26 " pdb=" C ILE J 26 " pdb=" CB ILE J 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 287 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 28 " -0.004 2.00e-02 2.50e+03 7.26e-03 5.27e-01 pdb=" C SER F 28 " 0.013 2.00e-02 2.50e+03 pdb=" O SER F 28 " -0.005 2.00e-02 2.50e+03 pdb=" N SER F 29 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 28 " -0.004 2.00e-02 2.50e+03 7.25e-03 5.26e-01 pdb=" C SER D 28 " 0.013 2.00e-02 2.50e+03 pdb=" O SER D 28 " -0.005 2.00e-02 2.50e+03 pdb=" N SER D 29 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 28 " 0.004 2.00e-02 2.50e+03 7.11e-03 5.06e-01 pdb=" C SER I 28 " -0.012 2.00e-02 2.50e+03 pdb=" O SER I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N SER I 29 " 0.004 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 757 2.88 - 3.38: 1501 3.38 - 3.89: 3175 3.89 - 4.39: 3586 4.39 - 4.90: 7029 Nonbonded interactions: 16048 Sorted by model distance: nonbonded pdb=" O SER A 19 " pdb=" ND2 ASN A 21 " model vdw 2.374 3.120 nonbonded pdb=" O SER G 19 " pdb=" ND2 ASN G 21 " model vdw 2.374 3.120 nonbonded pdb=" O SER J 19 " pdb=" ND2 ASN J 21 " model vdw 2.375 3.120 nonbonded pdb=" O SER E 19 " pdb=" ND2 ASN E 21 " model vdw 2.375 3.120 nonbonded pdb=" O SER C 19 " pdb=" ND2 ASN C 21 " model vdw 2.375 3.120 ... (remaining 16043 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 1.540 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.017 1850 Z= 0.256 Angle : 0.577 4.255 2510 Z= 0.355 Chirality : 0.041 0.118 290 Planarity : 0.002 0.007 330 Dihedral : 10.899 38.181 570 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.002 0.001 PHE F 23 TYR 0.001 0.001 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0820 time to fit residues: 1.3732 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077250 restraints weight = 2180.586| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.51 r_work: 0.3261 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1850 Z= 0.238 Angle : 0.483 2.852 2510 Z= 0.281 Chirality : 0.044 0.124 290 Planarity : 0.002 0.005 330 Dihedral : 4.277 12.740 250 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.005 0.001 PHE C 23 TYR 0.006 0.001 TYR A 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0866 time to fit residues: 1.3352 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 35 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN J 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081951 restraints weight = 2130.747| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.56 r_work: 0.3318 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 1850 Z= 0.457 Angle : 0.559 3.152 2510 Z= 0.335 Chirality : 0.048 0.122 290 Planarity : 0.003 0.007 330 Dihedral : 5.395 16.157 250 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 18 PHE 0.009 0.002 PHE H 23 TYR 0.009 0.002 TYR A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0937 time to fit residues: 1.4243 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.076815 restraints weight = 2101.276| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.59 r_work: 0.3253 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1850 Z= 0.269 Angle : 0.477 2.993 2510 Z= 0.283 Chirality : 0.045 0.124 290 Planarity : 0.002 0.005 330 Dihedral : 4.637 14.733 250 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 18 PHE 0.005 0.001 PHE H 23 TYR 0.010 0.002 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0871 time to fit residues: 1.3436 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073071 restraints weight = 2367.044| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.75 r_work: 0.3203 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 1850 Z= 0.669 Angle : 0.634 3.617 2510 Z= 0.385 Chirality : 0.052 0.122 290 Planarity : 0.003 0.009 330 Dihedral : 6.056 18.300 250 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.19 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS E 18 PHE 0.013 0.002 PHE H 23 TYR 0.011 0.003 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0912 time to fit residues: 1.3889 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079577 restraints weight = 2782.410| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.97 r_work: 0.3285 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1850 Z= 0.142 Angle : 0.447 2.778 2510 Z= 0.264 Chirality : 0.044 0.129 290 Planarity : 0.001 0.004 330 Dihedral : 4.264 14.065 250 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.003 0.000 PHE I 15 TYR 0.010 0.001 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1054 time to fit residues: 1.6228 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.084987 restraints weight = 2367.675| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.85 r_work: 0.3375 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1850 Z= 0.275 Angle : 0.477 2.987 2510 Z= 0.284 Chirality : 0.045 0.124 290 Planarity : 0.002 0.004 330 Dihedral : 4.702 15.365 250 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.21 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.004 0.001 PHE H 23 TYR 0.011 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0873 time to fit residues: 1.3397 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079848 restraints weight = 2625.001| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.93 r_work: 0.3304 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1850 Z= 0.162 Angle : 0.441 3.163 2510 Z= 0.259 Chirality : 0.044 0.126 290 Planarity : 0.001 0.004 330 Dihedral : 4.156 13.840 250 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.17 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.002 0.000 PHE G 15 TYR 0.010 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0891 time to fit residues: 1.3664 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082757 restraints weight = 2353.818| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.82 r_work: 0.3136 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1850 Z= 0.252 Angle : 0.465 3.277 2510 Z= 0.276 Chirality : 0.045 0.125 290 Planarity : 0.002 0.004 330 Dihedral : 4.557 14.994 250 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.004 0.001 PHE H 23 TYR 0.010 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0826 time to fit residues: 1.2530 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076165 restraints weight = 3010.372| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.14 r_work: 0.3072 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1850 Z= 0.296 Angle : 0.481 3.438 2510 Z= 0.287 Chirality : 0.045 0.124 290 Planarity : 0.002 0.005 330 Dihedral : 4.758 15.567 250 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.005 0.001 PHE H 23 TYR 0.010 0.002 TYR B 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0869 time to fit residues: 1.3256 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.082658 restraints weight = 2811.078| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.07 r_work: 0.3300 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1850 Z= 0.153 Angle : 0.441 3.605 2510 Z= 0.259 Chirality : 0.044 0.126 290 Planarity : 0.001 0.004 330 Dihedral : 4.137 13.857 250 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.17 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.003 0.001 PHE I 15 TYR 0.010 0.001 TYR B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.43 seconds wall clock time: 26 minutes 39.17 seconds (1599.17 seconds total)