Starting phenix.real_space_refine on Mon Feb 10 19:44:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az1_15729/02_2025/8az1_15729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az1_15729/02_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_15729/02_2025/8az1_15729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az1_15729/02_2025/8az1_15729.map" model { file = "/net/cci-nas-00/data/ceres_data/8az1_15729/02_2025/8az1_15729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az1_15729/02_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-5592/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: 0.76, per 1000 atoms: 0.42 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: 1.12 Conformation dependent library (CDL) restraints added in 218.9 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: 0.44 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: 1.16 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.990 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0901 time to fit residues: 1.4913 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=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 = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.077181 restraints weight = 2180.586| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.52 r_work: 0.3264 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0845 time to fit residues: 1.2872 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 : 0.179 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.9980 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.090926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073769 restraints weight = 2162.953| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.57 r_work: 0.3200 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1850 Z= 0.409 Angle : 0.542 3.144 2510 Z= 0.322 Chirality : 0.047 0.122 290 Planarity : 0.002 0.006 330 Dihedral : 5.225 15.695 250 Min Nonbonded Distance : 2.662 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: -1.69 (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 0.006 0.003 HIS A 18 PHE 0.008 0.002 PHE J 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 : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0887 time to fit residues: 1.3649 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=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: 2.9990 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.098517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081431 restraints weight = 2237.854| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.64 r_work: 0.3324 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2437 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= 0.458 Angle : 0.547 3.314 2510 Z= 0.329 Chirality : 0.048 0.124 290 Planarity : 0.003 0.007 330 Dihedral : 5.436 16.456 250 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.00 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: -1.85 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS F 18 PHE 0.009 0.002 PHE C 23 TYR 0.011 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 : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0711 time to fit residues: 1.0863 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 : 0.191 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075147 restraints weight = 2539.600| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.86 r_work: 0.3225 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.032 1850 Z= 0.510 Angle : 0.574 3.390 2510 Z= 0.347 Chirality : 0.048 0.123 290 Planarity : 0.003 0.008 330 Dihedral : 5.697 17.318 250 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % 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: -2.16 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS E 18 PHE 0.009 0.002 PHE H 23 TYR 0.011 0.002 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 : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0849 time to fit residues: 1.2852 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** 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 = 0.3571 r_free = 0.3571 target = 0.099874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079373 restraints weight = 2810.361| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.12 r_work: 0.3256 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2599 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= 0.157 Angle : 0.454 3.019 2510 Z= 0.269 Chirality : 0.044 0.128 290 Planarity : 0.001 0.004 330 Dihedral : 4.433 14.377 250 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 4.00 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: -2.14 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.003 0.000 PHE I 15 TYR 0.009 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 : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0901 time to fit residues: 1.3999 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 : 0.183 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** ** 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 = 0.3437 r_free = 0.3437 target = 0.094434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074550 restraints weight = 2889.274| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.08 r_work: 0.3063 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1850 Z= 0.403 Angle : 0.526 3.325 2510 Z= 0.316 Chirality : 0.047 0.123 290 Planarity : 0.002 0.006 330 Dihedral : 5.225 16.416 250 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % 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: -2.26 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS F 18 PHE 0.007 0.001 PHE C 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 : 0.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0911 time to fit residues: 1.3934 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 : 0.203 ------------------------------------------------------------------------------- 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: 8.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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** ** 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 = 0.3584 r_free = 0.3584 target = 0.100017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079739 restraints weight = 3074.775| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.19 r_work: 0.3285 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2621 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= 0.144 Angle : 0.447 3.255 2510 Z= 0.264 Chirality : 0.044 0.128 290 Planarity : 0.001 0.004 330 Dihedral : 4.258 14.123 250 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % 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 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (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 : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0971 time to fit residues: 1.4528 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 ------------------------------------------------------------------------------- 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: 0.0570 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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** ** 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 = 0.3605 r_free = 0.3605 target = 0.101062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081890 restraints weight = 2517.909| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.89 r_work: 0.3325 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2709 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= 0.137 Angle : 0.434 3.281 2510 Z= 0.253 Chirality : 0.044 0.126 290 Planarity : 0.001 0.004 330 Dihedral : 3.983 13.059 250 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % 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: -2.15 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.002 0.000 PHE I 15 TYR 0.009 0.001 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: 0.0880 time to fit residues: 1.3370 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 : 0.148 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079460 restraints weight = 2886.463| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.01 r_work: 0.3063 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1850 Z= 0.403 Angle : 0.516 3.340 2510 Z= 0.311 Chirality : 0.047 0.122 290 Planarity : 0.002 0.006 330 Dihedral : 5.113 16.512 250 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -2.22 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 18 PHE 0.008 0.001 PHE H 23 TYR 0.011 0.002 TYR F 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 : 0.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0903 time to fit residues: 1.3695 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 : 0.198 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3590 r_free = 0.3590 target = 0.100897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082054 restraints weight = 2669.152| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.95 r_work: 0.3110 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2803 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= 0.246 Angle : 0.469 3.102 2510 Z= 0.279 Chirality : 0.045 0.127 290 Planarity : 0.002 0.004 330 Dihedral : 4.680 15.425 250 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % 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: -2.22 (0.44), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 18 PHE 0.004 0.001 PHE H 23 TYR 0.011 0.002 TYR B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1480.38 seconds wall clock time: 27 minutes 1.14 seconds (1621.14 seconds total)