Starting phenix.real_space_refine on Tue Feb 13 08:28:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/02_2024/8de8_27387_updated.pdb" } resolution = 2.82 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= 0.002 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 4 5.49 5 S 16 5.16 5 C 3014 2.51 5 N 676 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4498 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2168 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2168 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'D21': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {' K': 4, 'D21': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 3.06, per 1000 atoms: 0.68 Number of scatterers: 4498 At special positions: 0 Unit cell: (90.738, 85.626, 94.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 16 16.00 P 4 15.00 O 784 8.00 N 676 7.00 C 3014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS A 93 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 845.4 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'B' and resid 44 through 90 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 153 through 198 Proline residue: B 168 - end of helix removed outlier: 4.826A pdb=" N LYS B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.735A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 Processing helix chain 'B' and resid 270 through 314 removed outlier: 3.656A pdb=" N ALA B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 90 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 153 through 198 Proline residue: A 168 - end of helix removed outlier: 4.826A pdb=" N LYS A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.735A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 270 through 314 removed outlier: 3.657A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 1002 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: 1.15 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 676 1.32 - 1.44: 1268 1.44 - 1.57: 2618 1.57 - 1.70: 12 1.70 - 1.83: 26 Bond restraints: 4600 Sorted by residual: bond pdb=" C33 D21 A 402 " pdb=" C34 D21 A 402 " ideal model delta sigma weight residual 1.532 1.585 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C33 D21 B 402 " pdb=" C34 D21 B 402 " ideal model delta sigma weight residual 1.532 1.584 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" C33 D21 A 401 " pdb=" C34 D21 A 401 " ideal model delta sigma weight residual 1.532 1.584 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C33 D21 B 401 " pdb=" C34 D21 B 401 " ideal model delta sigma weight residual 1.532 1.583 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C ILE B 299 " pdb=" O ILE B 299 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.23e-02 6.61e+03 5.65e+00 ... (remaining 4595 not shown) Histogram of bond angle deviations from ideal: 98.87 - 110.34: 946 110.34 - 121.81: 4493 121.81 - 133.29: 749 133.29 - 144.76: 14 144.76 - 156.23: 8 Bond angle restraints: 6210 Sorted by residual: angle pdb=" C40 D21 A 402 " pdb=" C41 D21 A 402 " pdb=" C42 D21 A 402 " ideal model delta sigma weight residual 120.01 156.23 -36.22 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C40 D21 B 402 " pdb=" C41 D21 B 402 " pdb=" C42 D21 B 402 " ideal model delta sigma weight residual 120.01 156.17 -36.16 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C39 D21 B 402 " pdb=" C40 D21 B 402 " pdb=" C41 D21 B 402 " ideal model delta sigma weight residual 120.02 156.11 -36.09 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C39 D21 A 402 " pdb=" C40 D21 A 402 " pdb=" C41 D21 A 402 " ideal model delta sigma weight residual 120.02 156.05 -36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C39 D21 B 401 " pdb=" C40 D21 B 401 " pdb=" C41 D21 B 401 " ideal model delta sigma weight residual 120.02 154.72 -34.70 3.00e+00 1.11e-01 1.34e+02 ... (remaining 6205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 2521 31.09 - 62.18: 110 62.18 - 93.28: 20 93.28 - 124.37: 0 124.37 - 155.46: 2 Dihedral angle restraints: 2653 sinusoidal: 1083 harmonic: 1570 Sorted by residual: dihedral pdb=" C06 D21 A 402 " pdb=" C07 D21 A 402 " pdb=" C08 D21 A 402 " pdb=" C09 D21 A 402 " ideal model delta sinusoidal sigma weight residual -134.99 20.47 -155.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C06 D21 B 402 " pdb=" C07 D21 B 402 " pdb=" C08 D21 B 402 " pdb=" C09 D21 B 402 " ideal model delta sinusoidal sigma weight residual -134.99 20.47 -155.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CG ARG B 111 " pdb=" CD ARG B 111 " pdb=" NE ARG B 111 " pdb=" CZ ARG B 111 " ideal model delta sinusoidal sigma weight residual 180.00 135.77 44.23 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 2650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 581 0.065 - 0.129: 103 0.129 - 0.193: 24 0.193 - 0.258: 0 0.258 - 0.322: 2 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB ILE B 264 " pdb=" CA ILE B 264 " pdb=" CG1 ILE B 264 " pdb=" CG2 ILE B 264 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A 264 " pdb=" CA ILE A 264 " pdb=" CG1 ILE A 264 " pdb=" CG2 ILE A 264 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB VAL B 41 " pdb=" CA VAL B 41 " pdb=" CG1 VAL B 41 " pdb=" CG2 VAL B 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 707 not shown) Planarity restraints: 742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 271 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 272 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 271 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 272 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 149 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO B 150 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.033 5.00e-02 4.00e+02 ... (remaining 739 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 960 2.79 - 3.38: 5333 3.38 - 3.96: 8330 3.96 - 4.55: 11373 4.55 - 5.14: 16843 Nonbonded interactions: 42839 Sorted by model distance: nonbonded pdb=" O ARG B 297 " pdb=" OG SER B 300 " model vdw 2.200 2.440 nonbonded pdb=" O GLY B 137 " pdb=" OG1 THR B 141 " model vdw 2.205 2.440 nonbonded pdb=" O GLY A 137 " pdb=" OG1 THR A 141 " model vdw 2.205 2.440 nonbonded pdb=" O ARG A 297 " pdb=" OG SER A 300 " model vdw 2.248 2.440 nonbonded pdb=" OE1 GLN A 76 " pdb=" NH2 ARG A 79 " model vdw 2.305 2.520 ... (remaining 42834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 315 or resid 401 through 402)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 1.710 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 4600 Z= 0.371 Angle : 1.628 36.221 6210 Z= 0.661 Chirality : 0.054 0.322 710 Planarity : 0.008 0.064 742 Dihedral : 17.888 155.459 1646 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.43 % Allowed : 0.86 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.33), residues: 548 helix: 2.16 (0.23), residues: 436 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 275 HIS 0.012 0.002 HIS A 313 PHE 0.027 0.003 PHE A 285 TYR 0.018 0.003 TYR A 78 ARG 0.003 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 0.474 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 195 average time/residue: 0.9025 time to fit residues: 183.7476 Evaluate side-chains 133 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain A residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 95 GLN B 115 ASN B 122 GLN B 313 HIS A 76 GLN A 95 GLN A 115 ASN A 122 GLN A 313 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4600 Z= 0.243 Angle : 0.716 11.417 6210 Z= 0.352 Chirality : 0.040 0.130 710 Planarity : 0.005 0.041 742 Dihedral : 17.064 172.786 692 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.45 % Allowed : 20.69 % Favored : 75.86 % 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: 3.33 (0.36), residues: 548 helix: 3.02 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 275 HIS 0.004 0.001 HIS B 313 PHE 0.012 0.001 PHE A 158 TYR 0.015 0.002 TYR A 78 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.479 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 149 average time/residue: 0.9411 time to fit residues: 146.1433 Evaluate side-chains 139 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 0.0010 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4600 Z= 0.243 Angle : 0.683 9.023 6210 Z= 0.335 Chirality : 0.039 0.129 710 Planarity : 0.004 0.037 742 Dihedral : 16.425 169.790 688 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.19 % Favored : 97.45 % Rotamer: Outliers : 3.45 % Allowed : 21.12 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.36), residues: 548 helix: 3.18 (0.24), residues: 436 sheet: None (None), residues: 0 loop : -1.77 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 275 HIS 0.002 0.001 HIS B 151 PHE 0.019 0.001 PHE B 214 TYR 0.011 0.002 TYR A 243 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.753 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 140 average time/residue: 0.9970 time to fit residues: 145.6571 Evaluate side-chains 120 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4600 Z= 0.251 Angle : 0.698 9.438 6210 Z= 0.339 Chirality : 0.040 0.129 710 Planarity : 0.004 0.036 742 Dihedral : 16.274 167.187 688 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.92 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 21.55 % Favored : 75.00 % 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: 3.46 (0.37), residues: 548 helix: 3.17 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -1.72 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 275 HIS 0.007 0.001 HIS A 91 PHE 0.012 0.001 PHE B 158 TYR 0.011 0.002 TYR A 243 ARG 0.006 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.477 Fit side-chains outliers start: 16 outliers final: 2 residues processed: 123 average time/residue: 0.8304 time to fit residues: 107.1723 Evaluate side-chains 110 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain A residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4600 Z= 0.266 Angle : 0.713 9.593 6210 Z= 0.342 Chirality : 0.039 0.126 710 Planarity : 0.004 0.037 742 Dihedral : 15.896 162.315 688 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.92 % Favored : 96.72 % Rotamer: Outliers : 3.02 % Allowed : 22.63 % Favored : 74.35 % 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: 3.49 (0.36), residues: 548 helix: 3.18 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -1.62 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 275 HIS 0.007 0.001 HIS A 91 PHE 0.026 0.002 PHE B 214 TYR 0.012 0.002 TYR A 243 ARG 0.006 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.519 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 133 average time/residue: 0.8422 time to fit residues: 117.6320 Evaluate side-chains 129 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 122 GLN A 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4600 Z= 0.249 Angle : 0.730 10.995 6210 Z= 0.357 Chirality : 0.039 0.128 710 Planarity : 0.004 0.034 742 Dihedral : 15.443 153.774 688 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.55 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 24.35 % Favored : 73.06 % 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: 3.48 (0.36), residues: 548 helix: 3.21 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -1.68 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 275 HIS 0.006 0.001 HIS B 91 PHE 0.012 0.001 PHE A 158 TYR 0.011 0.001 TYR B 162 ARG 0.007 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 1.0313 time to fit residues: 139.4891 Evaluate side-chains 117 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS A 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4600 Z= 0.260 Angle : 0.807 11.322 6210 Z= 0.385 Chirality : 0.039 0.127 710 Planarity : 0.004 0.036 742 Dihedral : 14.992 142.122 688 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.92 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 26.94 % Favored : 69.61 % 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: 3.50 (0.37), residues: 548 helix: 3.24 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -1.67 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 275 HIS 0.005 0.001 HIS B 91 PHE 0.026 0.001 PHE B 214 TYR 0.011 0.002 TYR B 162 ARG 0.007 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.544 Fit side-chains REVERT: A 126 MET cc_start: 0.7154 (tmm) cc_final: 0.6841 (tmm) outliers start: 16 outliers final: 6 residues processed: 123 average time/residue: 0.9097 time to fit residues: 117.1839 Evaluate side-chains 117 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4600 Z= 0.286 Angle : 0.805 12.179 6210 Z= 0.388 Chirality : 0.040 0.142 710 Planarity : 0.004 0.038 742 Dihedral : 14.713 127.831 688 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.10 % Favored : 96.53 % Rotamer: Outliers : 3.88 % Allowed : 24.57 % Favored : 71.55 % 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: 3.47 (0.37), residues: 548 helix: 3.19 (0.25), residues: 434 sheet: None (None), residues: 0 loop : -1.58 (0.53), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 275 HIS 0.007 0.001 HIS B 91 PHE 0.022 0.001 PHE B 214 TYR 0.012 0.002 TYR B 243 ARG 0.007 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.567 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.9268 time to fit residues: 123.3809 Evaluate side-chains 127 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN A 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4600 Z= 0.316 Angle : 0.868 13.062 6210 Z= 0.417 Chirality : 0.041 0.148 710 Planarity : 0.004 0.040 742 Dihedral : 14.358 114.467 688 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.47 % Favored : 96.17 % Rotamer: Outliers : 3.02 % Allowed : 25.43 % Favored : 71.55 % 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: 3.26 (0.36), residues: 548 helix: 3.04 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -1.55 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 275 HIS 0.011 0.001 HIS B 91 PHE 0.022 0.001 PHE A 214 TYR 0.011 0.002 TYR A 243 ARG 0.008 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.525 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.9493 time to fit residues: 123.0681 Evaluate side-chains 118 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.0010 chunk 42 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4600 Z= 0.237 Angle : 0.813 12.974 6210 Z= 0.395 Chirality : 0.040 0.140 710 Planarity : 0.004 0.041 742 Dihedral : 13.876 104.095 688 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.47 % Favored : 96.17 % Rotamer: Outliers : 2.59 % Allowed : 26.94 % Favored : 70.47 % 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: 3.40 (0.36), residues: 548 helix: 3.06 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -1.24 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 275 HIS 0.019 0.002 HIS B 91 PHE 0.021 0.001 PHE B 214 TYR 0.011 0.001 TYR A 162 ARG 0.009 0.001 ARG B 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.484 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.9449 time to fit residues: 111.7489 Evaluate side-chains 112 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087933 restraints weight = 6191.706| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.73 r_work: 0.2897 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4600 Z= 0.281 Angle : 0.827 13.216 6210 Z= 0.402 Chirality : 0.041 0.140 710 Planarity : 0.004 0.040 742 Dihedral : 13.653 94.925 688 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.47 % Favored : 96.17 % Rotamer: Outliers : 2.59 % Allowed : 26.29 % Favored : 71.12 % 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: 3.31 (0.37), residues: 548 helix: 2.99 (0.25), residues: 434 sheet: None (None), residues: 0 loop : -1.22 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 275 HIS 0.016 0.002 HIS B 91 PHE 0.020 0.001 PHE B 214 TYR 0.010 0.001 TYR A 243 ARG 0.009 0.001 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.77 seconds wall clock time: 43 minutes 27.49 seconds (2607.49 seconds total)