Starting phenix.real_space_refine on Tue Feb 13 20:42:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0o_15790/02_2024/8b0o_15790_updated.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3652 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2634 2.51 5 N 658 2.21 5 O 689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3995 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3995 Unusual residues: {'OJF': 1} Classifications: {'peptide': 506, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 36, 'TRANS': 469, None: 1} Not linked: pdbres="ARG A 508 " pdbres="OJF A 601 " Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 2.84, per 1000 atoms: 0.71 Number of scatterers: 3995 At special positions: 0 Unit cell: (58.646, 81.774, 85.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 689 8.00 N 658 7.00 C 2634 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 - 3.50 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: 1.67 Conformation dependent library (CDL) restraints added in 732.6 milliseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 3 sheets defined 46.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.722A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.566A pdb=" N ILE A 38 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 42 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 45 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.710A pdb=" N ALA A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 removed outlier: 4.387A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 161 through 167 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 169 through 189 Processing helix chain 'A' and resid 192 through 210 Proline residue: A 205 - end of helix removed outlier: 4.684A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.735A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.684A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 433 removed outlier: 4.326A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 489 through 507 Processing sheet with id= A, first strand: chain 'A' and resid 222 through 228 removed outlier: 3.548A pdb=" N GLU A 468 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 262 through 264 removed outlier: 6.340A pdb=" N SER A 294 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 382 through 384 removed outlier: 7.241A pdb=" N TYR A 406 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 460 " --> pdb=" O VAL A 451 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 429 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: 1.03 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 639 1.32 - 1.44: 1116 1.44 - 1.57: 2326 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4107 Sorted by residual: bond pdb=" C59 OJF A 601 " pdb=" N3 OJF A 601 " ideal model delta sigma weight residual 1.508 1.338 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C65 OJF A 601 " pdb=" N4 OJF A 601 " ideal model delta sigma weight residual 1.486 1.335 0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C53 OJF A 601 " pdb=" N1 OJF A 601 " ideal model delta sigma weight residual 1.488 1.339 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C56 OJF A 601 " pdb=" N2 OJF A 601 " ideal model delta sigma weight residual 1.484 1.338 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" N OJF A 601 " pdb=" C15 OJF A 601 " ideal model delta sigma weight residual 1.463 1.336 0.127 2.00e-02 2.50e+03 4.02e+01 ... (remaining 4102 not shown) Histogram of bond angle deviations from ideal: 100.25 - 106.99: 180 106.99 - 113.73: 2241 113.73 - 120.48: 1574 120.48 - 127.22: 1542 127.22 - 133.97: 68 Bond angle restraints: 5605 Sorted by residual: angle pdb=" C17 OJF A 601 " pdb=" S OJF A 601 " pdb=" C18 OJF A 601 " ideal model delta sigma weight residual 109.56 100.25 9.31 3.00e+00 1.11e-01 9.64e+00 angle pdb=" C38 OJF A 601 " pdb=" C37 OJF A 601 " pdb=" O3 OJF A 601 " ideal model delta sigma weight residual 120.03 111.02 9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" C22 OJF A 601 " pdb=" C21 OJF A 601 " pdb=" O1 OJF A 601 " ideal model delta sigma weight residual 119.89 111.23 8.66 3.00e+00 1.11e-01 8.33e+00 angle pdb=" C PRO A 53 " pdb=" N LEU A 54 " pdb=" CA LEU A 54 " ideal model delta sigma weight residual 121.54 126.90 -5.36 1.91e+00 2.74e-01 7.87e+00 angle pdb=" N TRP A 34 " pdb=" CA TRP A 34 " pdb=" C TRP A 34 " ideal model delta sigma weight residual 109.81 114.35 -4.54 2.21e+00 2.05e-01 4.23e+00 ... (remaining 5600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 2370 35.00 - 70.00: 23 70.00 - 105.00: 9 105.00 - 140.00: 0 140.00 - 175.00: 1 Dihedral angle restraints: 2403 sinusoidal: 949 harmonic: 1454 Sorted by residual: dihedral pdb=" C53 OJF A 601 " pdb=" C54 OJF A 601 " pdb=" N1 OJF A 601 " pdb=" C55 OJF A 601 " ideal model delta sinusoidal sigma weight residual 116.53 -68.47 -175.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA GLN A 45 " pdb=" C GLN A 45 " pdb=" N ALA A 46 " pdb=" CA ALA A 46 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C58 OJF A 601 " pdb=" C57 OJF A 601 " pdb=" C59 OJF A 601 " pdb=" N3 OJF A 601 " ideal model delta sinusoidal sigma weight residual 18.73 109.14 -90.41 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 472 0.046 - 0.092: 115 0.092 - 0.138: 43 0.138 - 0.184: 1 0.184 - 0.230: 1 Chirality restraints: 632 Sorted by residual: chirality pdb=" C54 OJF A 601 " pdb=" C55 OJF A 601 " pdb=" C56 OJF A 601 " pdb=" N1 OJF A 601 " both_signs ideal model delta sigma weight residual False 2.63 2.40 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" C57 OJF A 601 " pdb=" C58 OJF A 601 " pdb=" C59 OJF A 601 " pdb=" N2 OJF A 601 " both_signs ideal model delta sigma weight residual False 2.62 2.50 0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 629 not shown) Planarity restraints: 704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C54 OJF A 601 " 0.113 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C56 OJF A 601 " -0.091 2.00e-02 2.50e+03 pdb=" C57 OJF A 601 " 0.359 2.00e-02 2.50e+03 pdb=" N2 OJF A 601 " -0.545 2.00e-02 2.50e+03 pdb=" O7 OJF A 601 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N OJF A 601 " 0.522 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" O OJF A 601 " -0.101 2.00e-02 2.50e+03 pdb=" C14 OJF A 601 " -0.162 2.00e-02 2.50e+03 pdb=" C15 OJF A 601 " 0.087 2.00e-02 2.50e+03 pdb=" C16 OJF A 601 " -0.346 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 OJF A 601 " 0.173 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C53 OJF A 601 " -0.069 2.00e-02 2.50e+03 pdb=" C54 OJF A 601 " 0.262 2.00e-02 2.50e+03 pdb=" N1 OJF A 601 " -0.369 2.00e-02 2.50e+03 pdb=" O5 OJF A 601 " 0.003 2.00e-02 2.50e+03 ... (remaining 701 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 882 2.78 - 3.31: 3884 3.31 - 3.84: 6740 3.84 - 4.37: 8453 4.37 - 4.90: 14156 Nonbonded interactions: 34115 Sorted by model distance: nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.255 2.440 nonbonded pdb=" OG SER A 56 " pdb=" OG SER A 113 " model vdw 2.270 2.440 nonbonded pdb=" NH1 ARG A 13 " pdb=" O LEU A 47 " model vdw 2.302 2.520 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.321 2.440 nonbonded pdb=" OD2 ASP A 301 " pdb=" NH2 ARG A 332 " model vdw 2.331 2.520 ... (remaining 34110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 2.960 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 16.680 Find NCS groups from input model: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.009 0.170 4107 Z= 0.566 Angle : 0.703 9.315 5605 Z= 0.292 Chirality : 0.044 0.230 632 Planarity : 0.021 0.308 704 Dihedral : 12.960 174.996 1471 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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: -0.78 (0.38), residues: 504 helix: 0.22 (0.34), residues: 238 sheet: -0.83 (0.79), residues: 52 loop : -1.20 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.007 0.001 PHE A 28 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.451 Fit side-chains REVERT: A 90 ASN cc_start: 0.8270 (m-40) cc_final: 0.8019 (m-40) REVERT: A 133 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7483 (tp-100) REVERT: A 167 MET cc_start: 0.8523 (mtt) cc_final: 0.8272 (mtm) REVERT: A 276 ASN cc_start: 0.7331 (m110) cc_final: 0.7091 (m-40) REVERT: A 331 ASP cc_start: 0.7843 (m-30) cc_final: 0.7383 (p0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1802 time to fit residues: 18.8235 Evaluate side-chains 69 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 233 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4107 Z= 0.222 Angle : 0.669 11.780 5605 Z= 0.300 Chirality : 0.044 0.174 632 Planarity : 0.005 0.052 704 Dihedral : 14.040 137.221 605 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.00 % Allowed : 10.97 % Favored : 87.03 % 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: -0.53 (0.38), residues: 504 helix: 0.70 (0.35), residues: 222 sheet: -1.21 (0.75), residues: 51 loop : -1.15 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 492 HIS 0.001 0.001 HIS A 425 PHE 0.016 0.001 PHE A 174 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.456 Fit side-chains REVERT: A 276 ASN cc_start: 0.7337 (m110) cc_final: 0.7011 (m110) REVERT: A 291 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7345 (mttp) REVERT: A 331 ASP cc_start: 0.7897 (m-30) cc_final: 0.7329 (p0) outliers start: 8 outliers final: 3 residues processed: 78 average time/residue: 0.1494 time to fit residues: 15.0260 Evaluate side-chains 66 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 133 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4107 Z= 0.172 Angle : 0.598 9.578 5605 Z= 0.272 Chirality : 0.043 0.156 632 Planarity : 0.005 0.049 704 Dihedral : 13.523 140.816 605 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.00 % Allowed : 11.97 % Favored : 86.03 % 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: -0.50 (0.38), residues: 504 helix: 0.77 (0.35), residues: 223 sheet: -1.31 (0.71), residues: 56 loop : -1.16 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.001 0.000 HIS A 425 PHE 0.014 0.001 PHE A 174 TYR 0.007 0.001 TYR A 104 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.433 Fit side-chains REVERT: A 276 ASN cc_start: 0.7299 (m110) cc_final: 0.6970 (m110) REVERT: A 291 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7438 (mttp) REVERT: A 331 ASP cc_start: 0.7903 (m-30) cc_final: 0.7361 (p0) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.1602 time to fit residues: 13.7602 Evaluate side-chains 62 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 319 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4107 Z= 0.325 Angle : 0.655 9.959 5605 Z= 0.305 Chirality : 0.046 0.143 632 Planarity : 0.005 0.047 704 Dihedral : 13.230 139.066 605 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.49 % Allowed : 10.97 % Favored : 85.54 % 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: -0.85 (0.38), residues: 504 helix: 0.33 (0.34), residues: 232 sheet: -1.47 (0.70), residues: 56 loop : -1.22 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.016 0.002 PHE A 92 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.465 Fit side-chains REVERT: A 276 ASN cc_start: 0.7350 (m110) cc_final: 0.6962 (m110) REVERT: A 468 GLU cc_start: 0.7895 (tt0) cc_final: 0.7532 (tt0) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.1361 time to fit residues: 13.0357 Evaluate side-chains 70 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4107 Z= 0.166 Angle : 0.574 8.843 5605 Z= 0.265 Chirality : 0.043 0.137 632 Planarity : 0.005 0.046 704 Dihedral : 12.794 146.005 605 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.74 % Allowed : 12.97 % Favored : 84.29 % 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: -0.57 (0.39), residues: 504 helix: 0.69 (0.35), residues: 229 sheet: -1.56 (0.68), residues: 56 loop : -1.15 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.001 0.000 HIS A 337 PHE 0.018 0.001 PHE A 92 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.478 Fit side-chains REVERT: A 276 ASN cc_start: 0.7246 (m110) cc_final: 0.6903 (m110) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.1503 time to fit residues: 13.0649 Evaluate side-chains 66 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.0770 chunk 35 optimal weight: 7.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4107 Z= 0.202 Angle : 0.586 8.608 5605 Z= 0.272 Chirality : 0.044 0.139 632 Planarity : 0.005 0.045 704 Dihedral : 12.777 146.364 605 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.74 % Allowed : 14.71 % Favored : 82.54 % 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: -0.57 (0.39), residues: 504 helix: 0.71 (0.35), residues: 227 sheet: -1.59 (0.68), residues: 56 loop : -1.14 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 337 PHE 0.018 0.001 PHE A 92 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.406 Fit side-chains REVERT: A 276 ASN cc_start: 0.7268 (m110) cc_final: 0.6909 (m110) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.1353 time to fit residues: 11.3053 Evaluate side-chains 66 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4107 Z= 0.224 Angle : 0.590 8.198 5605 Z= 0.276 Chirality : 0.044 0.141 632 Planarity : 0.005 0.045 704 Dihedral : 12.904 148.935 605 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.99 % Allowed : 14.96 % Favored : 82.04 % 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: -0.59 (0.38), residues: 504 helix: 0.70 (0.35), residues: 227 sheet: -1.62 (0.67), residues: 56 loop : -1.15 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.018 0.001 PHE A 92 TYR 0.010 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.489 Fit side-chains REVERT: A 276 ASN cc_start: 0.7290 (m110) cc_final: 0.6926 (m110) outliers start: 12 outliers final: 12 residues processed: 66 average time/residue: 0.1413 time to fit residues: 12.2257 Evaluate side-chains 68 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4107 Z= 0.309 Angle : 0.628 8.498 5605 Z= 0.297 Chirality : 0.046 0.144 632 Planarity : 0.005 0.044 704 Dihedral : 13.082 146.535 605 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.99 % Allowed : 15.21 % Favored : 81.80 % 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: -0.71 (0.38), residues: 504 helix: 0.55 (0.35), residues: 227 sheet: -1.64 (0.68), residues: 56 loop : -1.17 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.019 0.002 PHE A 92 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.444 Fit side-chains REVERT: A 276 ASN cc_start: 0.7333 (m110) cc_final: 0.6929 (m110) REVERT: A 290 ASP cc_start: 0.8299 (t0) cc_final: 0.8045 (t0) REVERT: A 468 GLU cc_start: 0.7873 (tt0) cc_final: 0.7490 (tt0) outliers start: 12 outliers final: 12 residues processed: 64 average time/residue: 0.1318 time to fit residues: 11.2868 Evaluate side-chains 67 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 228 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4107 Z= 0.185 Angle : 0.566 7.207 5605 Z= 0.266 Chirality : 0.043 0.140 632 Planarity : 0.005 0.045 704 Dihedral : 13.016 155.288 605 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.99 % Allowed : 15.71 % Favored : 81.30 % 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: -0.51 (0.38), residues: 504 helix: 0.80 (0.35), residues: 227 sheet: -1.69 (0.67), residues: 56 loop : -1.12 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.001 0.000 HIS A 425 PHE 0.022 0.001 PHE A 92 TYR 0.008 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.431 Fit side-chains REVERT: A 276 ASN cc_start: 0.7273 (m110) cc_final: 0.6925 (m110) REVERT: A 290 ASP cc_start: 0.8263 (t0) cc_final: 0.8008 (t0) outliers start: 12 outliers final: 11 residues processed: 64 average time/residue: 0.1290 time to fit residues: 11.1186 Evaluate side-chains 67 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4107 Z= 0.184 Angle : 0.561 6.478 5605 Z= 0.266 Chirality : 0.043 0.137 632 Planarity : 0.005 0.045 704 Dihedral : 13.073 158.941 605 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.99 % Allowed : 14.96 % Favored : 82.04 % 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: -0.42 (0.39), residues: 504 helix: 0.89 (0.35), residues: 227 sheet: -1.66 (0.68), residues: 56 loop : -1.08 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.001 0.000 HIS A 337 PHE 0.026 0.001 PHE A 92 TYR 0.008 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.434 Fit side-chains REVERT: A 276 ASN cc_start: 0.7262 (m110) cc_final: 0.6917 (m110) REVERT: A 290 ASP cc_start: 0.8271 (t0) cc_final: 0.8014 (t0) outliers start: 12 outliers final: 11 residues processed: 67 average time/residue: 0.1257 time to fit residues: 11.2344 Evaluate side-chains 70 residues out of total 422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** A 395 GLN ** 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 = 0.3509 r_free = 0.3509 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113485 restraints weight = 5046.823| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.73 r_work: 0.3265 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4107 Z= 0.192 Angle : 0.560 6.265 5605 Z= 0.267 Chirality : 0.043 0.138 632 Planarity : 0.005 0.045 704 Dihedral : 13.045 160.090 605 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.24 % Allowed : 15.71 % Favored : 81.05 % 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: -0.43 (0.39), residues: 504 helix: 0.92 (0.36), residues: 227 sheet: -1.72 (0.67), residues: 56 loop : -1.11 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.029 0.001 PHE A 92 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1336.65 seconds wall clock time: 24 minutes 26.41 seconds (1466.41 seconds total)