Starting phenix.real_space_refine on Tue Feb 13 04:49:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex4_28650/02_2024/8ex4_28650_updated.pdb" } resolution = 2.93 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= 0.033 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 17 5.16 5 C 2122 2.51 5 N 532 2.21 5 O 554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" 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: 3226 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3226 Unusual residues: {'S1P': 1} Classifications: {'peptide': 417, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 404, None: 1} Not linked: pdbres="GLN A 539 " pdbres="S1P A 601 " Chain breaks: 2 Time building chain proxies: 2.25, per 1000 atoms: 0.70 Number of scatterers: 3226 At special positions: 0 Unit cell: (70.741, 68.794, 80.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 1 15.00 O 554 8.00 N 532 7.00 C 2122 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: 1.32 Conformation dependent library (CDL) restraints added in 599.2 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 120 through 133 removed outlier: 5.802A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 4.221A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 4.061A pdb=" N ASP A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.989A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.508A pdb=" N SER A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 224 through 256 removed outlier: 3.675A pdb=" N ALA A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 260 through 279 removed outlier: 4.306A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.658A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 346 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 390 removed outlier: 4.877A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 417 removed outlier: 3.781A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 438 through 450 removed outlier: 4.174A pdb=" N ALA A 441 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 442 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR A 443 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 444 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 4.820A pdb=" N ALA A 457 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 462 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 488 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 494 through 537 removed outlier: 4.411A pdb=" N LEU A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.598A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 922 1.34 - 1.45: 541 1.45 - 1.57: 1809 1.57 - 1.69: 1 1.69 - 1.81: 26 Bond restraints: 3299 Sorted by residual: bond pdb=" O1 S1P A 601 " pdb=" P22 S1P A 601 " ideal model delta sigma weight residual 1.661 1.607 0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C11 S1P A 601 " pdb=" C12 S1P A 601 " ideal model delta sigma weight residual 1.573 1.521 0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C13 S1P A 601 " pdb=" C14 S1P A 601 " ideal model delta sigma weight residual 1.569 1.519 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C12 S1P A 601 " pdb=" C13 S1P A 601 " ideal model delta sigma weight residual 1.569 1.522 0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C5 S1P A 601 " pdb=" C6 S1P A 601 " ideal model delta sigma weight residual 1.550 1.506 0.044 2.00e-02 2.50e+03 4.95e+00 ... (remaining 3294 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.94: 72 106.94 - 113.69: 1856 113.69 - 120.45: 1370 120.45 - 127.21: 1142 127.21 - 133.97: 34 Bond angle restraints: 4474 Sorted by residual: angle pdb=" C ILE A 175 " pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 111.81 107.03 4.78 1.25e+00 6.40e-01 1.46e+01 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 120.11 -6.51 1.90e+00 2.77e-01 1.17e+01 angle pdb=" N LYS A 102 " pdb=" CA LYS A 102 " pdb=" C LYS A 102 " ideal model delta sigma weight residual 112.23 108.32 3.91 1.26e+00 6.30e-01 9.63e+00 angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 109.81 114.21 -4.40 1.53e+00 4.27e-01 8.28e+00 angle pdb=" N THR A 226 " pdb=" CA THR A 226 " pdb=" C THR A 226 " ideal model delta sigma weight residual 111.28 108.19 3.09 1.09e+00 8.42e-01 8.01e+00 ... (remaining 4469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1745 17.88 - 35.77: 127 35.77 - 53.65: 19 53.65 - 71.53: 8 71.53 - 89.41: 5 Dihedral angle restraints: 1904 sinusoidal: 717 harmonic: 1187 Sorted by residual: dihedral pdb=" CA MET A 334 " pdb=" C MET A 334 " pdb=" N TRP A 335 " pdb=" CA TRP A 335 " ideal model delta harmonic sigma weight residual 180.00 -163.84 -16.16 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" C3 S1P A 601 " pdb=" C1 S1P A 601 " pdb=" C2 S1P A 601 " pdb=" O1 S1P A 601 " ideal model delta sinusoidal sigma weight residual 265.26 178.97 86.29 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CA ASP A 396 " pdb=" CB ASP A 396 " pdb=" CG ASP A 396 " pdb=" OD1 ASP A 396 " ideal model delta sinusoidal sigma weight residual -30.00 -83.71 53.71 1 2.00e+01 2.50e-03 9.80e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 371 0.042 - 0.083: 123 0.083 - 0.124: 28 0.124 - 0.165: 1 0.165 - 0.207: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA TRP A 178 " pdb=" N TRP A 178 " pdb=" C TRP A 178 " pdb=" CB TRP A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA SER A 266 " pdb=" N SER A 266 " pdb=" C SER A 266 " pdb=" CB SER A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 522 not shown) Planarity restraints: 544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " 0.014 2.00e-02 2.50e+03 1.02e-02 2.62e+00 pdb=" CG TRP A 178 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 266 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 267 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 509 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.017 5.00e-02 4.00e+02 ... (remaining 541 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 90 2.71 - 3.26: 3522 3.26 - 3.81: 5498 3.81 - 4.35: 7195 4.35 - 4.90: 11961 Nonbonded interactions: 28266 Sorted by model distance: nonbonded pdb=" O LEU A 127 " pdb=" NE2 GLN A 131 " model vdw 2.165 2.520 nonbonded pdb=" OH TYR A 246 " pdb=" O GLY A 333 " model vdw 2.217 2.440 nonbonded pdb=" OD1 ASP A 529 " pdb=" NH2 ARG A 532 " model vdw 2.248 2.520 nonbonded pdb=" O ILE A 369 " pdb=" OG1 THR A 373 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP A 484 " pdb=" NH2 ARG A 487 " model vdw 2.280 2.520 ... (remaining 28261 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.440 Find NCS groups from input model: 0.080 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.005 0.054 3299 Z= 0.350 Angle : 0.732 6.698 4474 Z= 0.425 Chirality : 0.043 0.207 525 Planarity : 0.004 0.030 544 Dihedral : 14.197 89.411 1144 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 0.40 (0.41), residues: 411 helix: 0.41 (0.27), residues: 363 sheet: None (None), residues: 0 loop : 0.08 (0.99), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.017 0.002 PHE A 236 TYR 0.013 0.001 TYR A 120 ARG 0.007 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.338 Fit side-chains REVERT: A 488 GLN cc_start: 0.7753 (mt0) cc_final: 0.7540 (mt0) outliers start: 0 outliers final: 1 residues processed: 57 average time/residue: 0.9856 time to fit residues: 58.2061 Evaluate side-chains 45 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3299 Z= 0.223 Angle : 0.546 8.466 4474 Z= 0.290 Chirality : 0.039 0.158 525 Planarity : 0.004 0.028 544 Dihedral : 8.529 71.608 466 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.08 % Allowed : 6.82 % Favored : 91.10 % 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: 0.98 (0.41), residues: 411 helix: 0.83 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -0.06 (1.04), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.025 0.002 PHE A 236 TYR 0.012 0.001 TYR A 120 ARG 0.007 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.319 Fit side-chains REVERT: A 488 GLN cc_start: 0.7663 (mt0) cc_final: 0.7429 (mt0) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.7562 time to fit residues: 37.2568 Evaluate side-chains 42 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 12 optimal weight: 0.0170 chunk 29 optimal weight: 0.0000 overall best weight: 0.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3299 Z= 0.135 Angle : 0.465 6.918 4474 Z= 0.248 Chirality : 0.036 0.146 525 Planarity : 0.004 0.028 544 Dihedral : 7.591 59.736 464 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.48 % Allowed : 10.09 % Favored : 88.43 % 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: 1.88 (0.42), residues: 411 helix: 1.42 (0.27), residues: 362 sheet: None (None), residues: 0 loop : 0.43 (0.99), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.022 0.001 PHE A 236 TYR 0.008 0.001 TYR A 120 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.367 Fit side-chains REVERT: A 405 LEU cc_start: 0.6859 (mt) cc_final: 0.6629 (mm) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.5921 time to fit residues: 27.6914 Evaluate side-chains 42 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3299 Z= 0.223 Angle : 0.523 7.959 4474 Z= 0.282 Chirality : 0.039 0.157 525 Planarity : 0.004 0.030 544 Dihedral : 7.726 58.199 464 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.67 % Allowed : 11.57 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.41), residues: 411 helix: 1.19 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.06 (1.05), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 178 HIS 0.003 0.001 HIS A 260 PHE 0.013 0.001 PHE A 327 TYR 0.011 0.001 TYR A 120 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.326 Fit side-chains REVERT: A 236 PHE cc_start: 0.7003 (t80) cc_final: 0.6771 (t80) REVERT: A 248 THR cc_start: 0.8153 (m) cc_final: 0.7873 (m) REVERT: A 488 GLN cc_start: 0.7643 (mt0) cc_final: 0.7364 (mt0) REVERT: A 507 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6305 (mp) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.7296 time to fit residues: 35.3309 Evaluate side-chains 49 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3299 Z= 0.181 Angle : 0.492 7.523 4474 Z= 0.266 Chirality : 0.037 0.155 525 Planarity : 0.004 0.030 544 Dihedral : 7.580 57.702 464 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 13.65 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.41), residues: 411 helix: 1.30 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.20 (1.04), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.011 0.001 PHE A 327 TYR 0.010 0.001 TYR A 120 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.355 Fit side-chains REVERT: A 236 PHE cc_start: 0.6916 (t80) cc_final: 0.6663 (t80) REVERT: A 248 THR cc_start: 0.8123 (m) cc_final: 0.7844 (m) REVERT: A 405 LEU cc_start: 0.6849 (mt) cc_final: 0.6641 (mm) REVERT: A 488 GLN cc_start: 0.7629 (mt0) cc_final: 0.7359 (mt0) REVERT: A 507 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6237 (mp) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.7739 time to fit residues: 37.5140 Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3299 Z= 0.206 Angle : 0.511 7.778 4474 Z= 0.274 Chirality : 0.038 0.158 525 Planarity : 0.004 0.032 544 Dihedral : 7.698 58.143 464 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 13.95 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.41), residues: 411 helix: 1.31 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 0.11 (1.01), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.011 0.001 PHE A 327 TYR 0.011 0.001 TYR A 120 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.341 Fit side-chains REVERT: A 236 PHE cc_start: 0.6966 (t80) cc_final: 0.6740 (t80) REVERT: A 248 THR cc_start: 0.8154 (m) cc_final: 0.7872 (m) REVERT: A 488 GLN cc_start: 0.7606 (mt0) cc_final: 0.7360 (mt0) REVERT: A 507 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6310 (mp) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.6775 time to fit residues: 32.8444 Evaluate side-chains 46 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3299 Z= 0.180 Angle : 0.498 7.456 4474 Z= 0.265 Chirality : 0.038 0.155 525 Planarity : 0.004 0.032 544 Dihedral : 7.659 59.648 464 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.97 % Allowed : 13.95 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.41), residues: 411 helix: 1.47 (0.27), residues: 361 sheet: None (None), residues: 0 loop : 0.40 (0.94), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.011 0.001 PHE A 327 TYR 0.010 0.001 TYR A 120 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.360 Fit side-chains REVERT: A 248 THR cc_start: 0.8134 (m) cc_final: 0.7846 (m) REVERT: A 507 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6238 (mp) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.7234 time to fit residues: 36.5923 Evaluate side-chains 49 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 488 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3299 Z= 0.238 Angle : 0.545 7.937 4474 Z= 0.288 Chirality : 0.041 0.236 525 Planarity : 0.004 0.033 544 Dihedral : 7.728 53.279 464 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.37 % Allowed : 15.13 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.41), residues: 411 helix: 1.22 (0.26), residues: 365 sheet: None (None), residues: 0 loop : 0.04 (0.98), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 178 HIS 0.003 0.001 HIS A 260 PHE 0.025 0.002 PHE A 236 TYR 0.012 0.001 TYR A 120 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.367 Fit side-chains REVERT: A 248 THR cc_start: 0.8204 (m) cc_final: 0.7947 (m) REVERT: A 375 PHE cc_start: 0.6082 (m-10) cc_final: 0.3886 (t80) REVERT: A 507 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6345 (mp) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.6281 time to fit residues: 29.4253 Evaluate side-chains 44 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3299 Z= 0.205 Angle : 0.529 7.673 4474 Z= 0.280 Chirality : 0.040 0.266 525 Planarity : 0.004 0.033 544 Dihedral : 7.703 54.125 464 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.67 % Allowed : 14.84 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.41), residues: 411 helix: 1.26 (0.26), residues: 367 sheet: None (None), residues: 0 loop : 0.28 (1.01), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 178 HIS 0.003 0.001 HIS A 260 PHE 0.025 0.001 PHE A 410 TYR 0.013 0.001 TYR A 120 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.371 Fit side-chains REVERT: A 248 THR cc_start: 0.8160 (m) cc_final: 0.7894 (m) REVERT: A 375 PHE cc_start: 0.5892 (m-10) cc_final: 0.3850 (t80) REVERT: A 507 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6318 (mp) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.6231 time to fit residues: 29.1915 Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3299 Z= 0.243 Angle : 0.555 7.993 4474 Z= 0.292 Chirality : 0.041 0.269 525 Planarity : 0.004 0.034 544 Dihedral : 7.750 50.988 464 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.67 % Allowed : 14.54 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.41), residues: 411 helix: 1.17 (0.26), residues: 367 sheet: None (None), residues: 0 loop : 0.25 (1.00), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 178 HIS 0.003 0.001 HIS A 260 PHE 0.025 0.002 PHE A 410 TYR 0.013 0.001 TYR A 120 ARG 0.002 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.346 Fit side-chains REVERT: A 248 THR cc_start: 0.8215 (m) cc_final: 0.7959 (m) REVERT: A 375 PHE cc_start: 0.5982 (m-10) cc_final: 0.3868 (t80) REVERT: A 507 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6347 (mp) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.5937 time to fit residues: 28.4340 Evaluate side-chains 44 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145478 restraints weight = 3271.653| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.14 r_work: 0.3493 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3299 Z= 0.225 Angle : 0.541 7.837 4474 Z= 0.286 Chirality : 0.041 0.261 525 Planarity : 0.004 0.034 544 Dihedral : 7.707 50.771 464 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.37 % Allowed : 14.84 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.41), residues: 411 helix: 1.20 (0.26), residues: 367 sheet: None (None), residues: 0 loop : 0.27 (1.00), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 178 HIS 0.003 0.001 HIS A 260 PHE 0.029 0.002 PHE A 236 TYR 0.012 0.001 TYR A 120 ARG 0.002 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1535.52 seconds wall clock time: 28 minutes 6.23 seconds (1686.23 seconds total)