Starting phenix.real_space_refine on Mon May 6 20:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrn_34979/05_2024/8hrn_34979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrn_34979/05_2024/8hrn_34979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrn_34979/05_2024/8hrn_34979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrn_34979/05_2024/8hrn_34979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrn_34979/05_2024/8hrn_34979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrn_34979/05_2024/8hrn_34979.pdb" } resolution = 3.9 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= 0.037 sd= 0.100 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 3.00, per 1000 atoms: 0.62 Number of scatterers: 4870 At special positions: 0 Unit cell: (84.0942, 85.1324, 71.6358, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 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: 1.82 Conformation dependent library (CDL) restraints added in 820.2 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.588A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.779A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.921A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.569A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.747A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.560A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.964A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.567A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.887A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.756A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 4.227A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.954A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.003A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.792A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.718A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.648A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.208A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.686A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.611A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.389A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.452A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.500A pdb=" N ALA A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 645 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: 1.22 Time building geometry restraints manager: 2.00 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: 1575 1.34 - 1.46: 1252 1.46 - 1.58: 2129 1.58 - 1.70: 1 1.70 - 1.82: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" CG PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.12e+00 bond pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.88e+00 bond pdb=" N PRO A 565 " pdb=" CA PRO A 565 " ideal model delta sigma weight residual 1.465 1.442 0.023 1.10e-02 8.26e+03 4.23e+00 bond pdb=" CG LEU A 595 " pdb=" CD1 LEU A 595 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 95.18 - 102.96: 38 102.96 - 110.75: 1526 110.75 - 118.54: 2325 118.54 - 126.32: 2797 126.32 - 134.11: 117 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 112.00 95.18 16.82 1.40e+00 5.10e-01 1.44e+02 angle pdb=" N PRO A 565 " pdb=" CD PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 103.20 95.37 7.83 1.50e+00 4.44e-01 2.72e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.30 119.20 4.10 1.06e+00 8.90e-01 1.49e+01 angle pdb=" CB LYS A 476 " pdb=" CG LYS A 476 " pdb=" CD LYS A 476 " ideal model delta sigma weight residual 111.30 119.28 -7.98 2.30e+00 1.89e-01 1.20e+01 angle pdb=" CA PRO A 565 " pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 104.50 98.19 6.31 1.90e+00 2.77e-01 1.10e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2518 17.90 - 35.80: 349 35.80 - 53.70: 70 53.70 - 71.59: 17 71.59 - 89.49: 5 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 49.70 43.30 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 135.56 -42.56 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 548 0.056 - 0.112: 145 0.112 - 0.167: 13 0.167 - 0.223: 3 0.223 - 0.279: 1 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" C PRO A 565 " pdb=" CB PRO A 565 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP A 206 " pdb=" N ASP A 206 " pdb=" C ASP A 206 " pdb=" CB ASP A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 564 " 0.099 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO A 565 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 137 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 138 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.003 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP A 478 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " -0.007 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 89 2.64 - 3.21: 4883 3.21 - 3.77: 8361 3.77 - 4.34: 11050 4.34 - 4.90: 17182 Nonbonded interactions: 41565 Sorted by model distance: nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.080 2.440 nonbonded pdb=" NE2 GLN A 81 " pdb=" OD1 ASN A 103 " model vdw 2.150 2.520 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.151 2.440 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 362 " model vdw 2.176 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.198 2.520 ... (remaining 41560 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 group one per residue 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 0.163 5007 Z= 0.295 Angle : 0.912 16.822 6803 Z= 0.532 Chirality : 0.050 0.279 710 Planarity : 0.007 0.135 881 Dihedral : 17.072 89.492 1820 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.95 % Allowed : 21.44 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.15 (0.35), residues: 595 helix: -0.62 (0.28), residues: 347 sheet: -1.41 (1.34), residues: 12 loop : -0.71 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 478 HIS 0.006 0.001 HIS A 417 PHE 0.020 0.002 PHE A 452 TYR 0.027 0.002 TYR A 385 ARG 0.005 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7403 (tmm) cc_final: 0.6907 (tmm) REVERT: A 391 LEU cc_start: 0.6794 (mt) cc_final: 0.6565 (mp) REVERT: A 476 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7146 (tppp) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.1903 time to fit residues: 15.9586 Evaluate side-chains 61 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 chunk 23 optimal weight: 0.0010 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5007 Z= 0.201 Angle : 0.645 9.820 6803 Z= 0.323 Chirality : 0.043 0.150 710 Planarity : 0.005 0.060 881 Dihedral : 5.290 53.312 649 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.66 % Allowed : 18.60 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.67 (0.36), residues: 595 helix: -0.20 (0.28), residues: 351 sheet: -1.51 (1.37), residues: 12 loop : -0.56 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.003 0.001 HIS A 417 PHE 0.015 0.002 PHE A 452 TYR 0.011 0.002 TYR A 516 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7596 (tmm) cc_final: 0.7077 (tmm) REVERT: A 340 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.5964 (pp30) REVERT: A 481 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6980 (ttpt) outliers start: 14 outliers final: 5 residues processed: 73 average time/residue: 0.1681 time to fit residues: 16.0498 Evaluate side-chains 66 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5007 Z= 0.194 Angle : 0.620 9.597 6803 Z= 0.306 Chirality : 0.041 0.125 710 Planarity : 0.004 0.046 881 Dihedral : 4.744 34.298 644 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.80 % Allowed : 18.98 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.47 (0.36), residues: 595 helix: -0.06 (0.29), residues: 352 sheet: -1.52 (1.34), residues: 12 loop : -0.41 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.003 0.001 HIS A 241 PHE 0.014 0.001 PHE A 452 TYR 0.026 0.002 TYR A 237 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7681 (tmm) cc_final: 0.7080 (tmm) REVERT: A 340 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6493 (pp30) REVERT: A 376 MET cc_start: 0.5259 (tpp) cc_final: 0.4956 (mmm) REVERT: A 471 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6482 (p0) REVERT: A 481 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6916 (ttpt) outliers start: 20 outliers final: 8 residues processed: 78 average time/residue: 0.1700 time to fit residues: 17.5704 Evaluate side-chains 69 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 508 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5007 Z= 0.318 Angle : 0.712 11.376 6803 Z= 0.360 Chirality : 0.045 0.172 710 Planarity : 0.005 0.046 881 Dihedral : 5.380 51.183 644 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.93 % Allowed : 20.49 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.68 (0.35), residues: 595 helix: -0.19 (0.28), residues: 349 sheet: -1.61 (1.32), residues: 12 loop : -0.58 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 165 HIS 0.010 0.002 HIS A 417 PHE 0.025 0.002 PHE A 452 TYR 0.024 0.003 TYR A 237 ARG 0.005 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7662 (ttp) cc_final: 0.7297 (mtm) REVERT: A 82 MET cc_start: 0.7804 (tmm) cc_final: 0.7139 (tmm) REVERT: A 340 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6170 (pp30) REVERT: A 398 GLU cc_start: 0.6560 (pt0) cc_final: 0.6319 (pt0) REVERT: A 477 TRP cc_start: 0.7574 (OUTLIER) cc_final: 0.6328 (t-100) REVERT: A 481 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6932 (pttm) outliers start: 26 outliers final: 9 residues processed: 84 average time/residue: 0.1626 time to fit residues: 17.9418 Evaluate side-chains 72 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 40.0000 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5007 Z= 0.230 Angle : 0.659 10.959 6803 Z= 0.327 Chirality : 0.043 0.155 710 Planarity : 0.004 0.042 881 Dihedral : 5.309 51.311 644 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.74 % Allowed : 23.72 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.44 (0.36), residues: 595 helix: -0.04 (0.29), residues: 351 sheet: -1.80 (1.27), residues: 12 loop : -0.38 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 203 HIS 0.007 0.001 HIS A 417 PHE 0.011 0.001 PHE A 452 TYR 0.018 0.002 TYR A 237 ARG 0.003 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7768 (tmm) cc_final: 0.7049 (tmm) REVERT: A 144 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7747 (tp) REVERT: A 340 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6243 (pp30) REVERT: A 376 MET cc_start: 0.5241 (tpp) cc_final: 0.5009 (mmm) REVERT: A 471 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6438 (p0) REVERT: A 481 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6472 (ttpt) outliers start: 25 outliers final: 10 residues processed: 84 average time/residue: 0.1665 time to fit residues: 18.3873 Evaluate side-chains 73 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5007 Z= 0.287 Angle : 0.723 10.902 6803 Z= 0.354 Chirality : 0.044 0.161 710 Planarity : 0.004 0.044 881 Dihedral : 5.573 56.491 644 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.93 % Allowed : 24.86 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.52 (0.35), residues: 595 helix: -0.11 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 203 HIS 0.005 0.001 HIS A 417 PHE 0.014 0.001 PHE A 452 TYR 0.020 0.002 TYR A 237 ARG 0.004 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 65 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7676 (ttp) cc_final: 0.7342 (mtm) REVERT: A 82 MET cc_start: 0.7744 (tmm) cc_final: 0.7123 (tmm) REVERT: A 144 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7610 (tp) REVERT: A 297 MET cc_start: 0.7426 (mpp) cc_final: 0.7215 (pmm) REVERT: A 340 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6488 (pp30) REVERT: A 366 MET cc_start: 0.5383 (mtt) cc_final: 0.4389 (mmm) REVERT: A 471 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6479 (p0) REVERT: A 477 TRP cc_start: 0.7558 (OUTLIER) cc_final: 0.6552 (t-100) REVERT: A 481 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6843 (ttpt) REVERT: A 515 TYR cc_start: 0.8018 (m-10) cc_final: 0.7661 (m-10) outliers start: 26 outliers final: 13 residues processed: 87 average time/residue: 0.1645 time to fit residues: 18.7975 Evaluate side-chains 75 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5007 Z= 0.236 Angle : 0.700 11.439 6803 Z= 0.339 Chirality : 0.044 0.204 710 Planarity : 0.004 0.040 881 Dihedral : 4.965 27.967 644 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.36 % Allowed : 25.05 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.49 (0.35), residues: 595 helix: -0.16 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 203 HIS 0.005 0.001 HIS A 417 PHE 0.012 0.001 PHE A 369 TYR 0.023 0.002 TYR A 237 ARG 0.005 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7780 (tmm) cc_final: 0.7153 (tmm) REVERT: A 144 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7765 (tp) REVERT: A 169 ARG cc_start: 0.6310 (mtt180) cc_final: 0.5598 (mtt180) REVERT: A 270 MET cc_start: 0.5900 (mmm) cc_final: 0.5076 (tmm) REVERT: A 340 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6603 (pp30) REVERT: A 471 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6345 (p0) REVERT: A 477 TRP cc_start: 0.7468 (OUTLIER) cc_final: 0.6690 (t-100) REVERT: A 481 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6743 (pttm) outliers start: 23 outliers final: 11 residues processed: 82 average time/residue: 0.1643 time to fit residues: 17.8484 Evaluate side-chains 74 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 578 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 0.0050 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5007 Z= 0.191 Angle : 0.667 12.285 6803 Z= 0.319 Chirality : 0.042 0.178 710 Planarity : 0.004 0.039 881 Dihedral : 4.652 17.675 642 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.80 % Allowed : 25.62 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.32 (0.36), residues: 595 helix: -0.09 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 203 HIS 0.005 0.001 HIS A 417 PHE 0.009 0.001 PHE A 369 TYR 0.027 0.002 TYR A 237 ARG 0.004 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7156 (mtm) REVERT: A 82 MET cc_start: 0.7932 (tmm) cc_final: 0.7430 (tmm) REVERT: A 471 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6422 (p0) REVERT: A 477 TRP cc_start: 0.7406 (OUTLIER) cc_final: 0.6561 (t-100) REVERT: A 481 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6364 (tttt) outliers start: 20 outliers final: 11 residues processed: 80 average time/residue: 0.1845 time to fit residues: 19.0383 Evaluate side-chains 73 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.189 > 50: distance: 57 - 63: 20.285 distance: 63 - 64: 9.189 distance: 64 - 65: 51.632 distance: 64 - 67: 18.980 distance: 65 - 66: 57.689 distance: 65 - 72: 9.487 distance: 67 - 68: 23.110 distance: 68 - 69: 13.324 distance: 69 - 70: 6.733 distance: 69 - 71: 4.291 distance: 72 - 73: 40.721 distance: 73 - 74: 19.466 distance: 74 - 75: 34.797 distance: 74 - 76: 21.254 distance: 76 - 77: 22.043 distance: 77 - 78: 31.756 distance: 77 - 80: 11.447 distance: 78 - 79: 16.476 distance: 78 - 87: 47.623 distance: 80 - 81: 18.840 distance: 81 - 82: 10.346 distance: 81 - 83: 10.118 distance: 83 - 85: 6.572 distance: 84 - 86: 3.730 distance: 85 - 86: 6.282 distance: 87 - 88: 21.385 distance: 88 - 89: 24.759 distance: 88 - 91: 29.580 distance: 89 - 90: 24.297 distance: 89 - 97: 15.978 distance: 90 - 118: 36.795 distance: 91 - 92: 34.856 distance: 92 - 93: 22.118 distance: 92 - 94: 29.311 distance: 93 - 95: 29.455 distance: 94 - 96: 16.366 distance: 95 - 96: 28.829 distance: 97 - 98: 29.408 distance: 98 - 99: 17.971 distance: 98 - 101: 17.438 distance: 99 - 100: 20.919 distance: 99 - 106: 12.313 distance: 101 - 102: 16.320 distance: 102 - 103: 10.980 distance: 103 - 104: 10.403 distance: 103 - 105: 11.497 distance: 106 - 107: 29.897 distance: 107 - 108: 4.048 distance: 107 - 110: 39.412 distance: 108 - 109: 38.975 distance: 108 - 111: 38.171 distance: 111 - 112: 34.103 distance: 112 - 113: 25.284 distance: 112 - 115: 27.633 distance: 113 - 114: 25.906 distance: 113 - 118: 33.687 distance: 115 - 116: 51.917 distance: 115 - 117: 32.413 distance: 118 - 119: 35.335 distance: 119 - 120: 16.042 distance: 120 - 121: 27.637 distance: 120 - 122: 18.747 distance: 122 - 123: 44.588 distance: 123 - 124: 14.472 distance: 123 - 126: 42.585 distance: 124 - 125: 50.282 distance: 124 - 131: 43.027 distance: 125 - 152: 18.722 distance: 126 - 127: 29.468 distance: 127 - 128: 14.700 distance: 128 - 129: 5.966 distance: 128 - 130: 8.906 distance: 131 - 132: 48.137 distance: 132 - 133: 42.985 distance: 132 - 135: 29.477 distance: 133 - 134: 22.195 distance: 133 - 139: 25.849 distance: 134 - 160: 27.799 distance: 135 - 136: 47.002 distance: 135 - 137: 35.019 distance: 136 - 138: 28.161 distance: 181 - 194: 3.000 distance: 197 - 215: 3.042 distance: 218 - 231: 3.081