Starting phenix.real_space_refine on Mon Mar 11 10:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/03_2024/8twi_41668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/03_2024/8twi_41668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/03_2024/8twi_41668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/03_2024/8twi_41668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/03_2024/8twi_41668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/03_2024/8twi_41668.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 S 26 5.16 5 C 2584 2.51 5 N 696 2.21 5 O 765 1.98 5 H 4023 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8096 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3096 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "C" Number of atoms: 4696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4696 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 284} Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 302 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.52 Number of scatterers: 8096 At special positions: 0 Unit cell: (77.43, 72.624, 86.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 26 16.00 O 765 8.00 N 696 7.00 C 2584 6.00 H 4023 1.00 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: 7.31 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 65.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.875A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.587A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.560A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 482 removed outlier: 3.792A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.610A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 520 removed outlier: 3.502A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.658A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.627A pdb=" N VAL C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.677A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.600A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.801A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.664A pdb=" N GLU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.204A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 220 hydrogen bonds defined for protein. 639 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: 2.91 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4010 1.03 - 1.23: 13 1.23 - 1.42: 1739 1.42 - 1.61: 2378 1.61 - 1.81: 39 Bond restraints: 8179 Sorted by residual: bond pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.75e+00 bond pdb=" N GLY A 396 " pdb=" CA GLY A 396 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00 bond pdb=" N ASP C 2 " pdb=" CA ASP C 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLY D 93 " pdb=" H GLY D 93 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" N GLY A 396 " pdb=" H GLY A 396 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 8174 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 269 107.34 - 113.99: 9654 113.99 - 120.65: 2792 120.65 - 127.30: 2010 127.30 - 133.96: 50 Bond angle restraints: 14775 Sorted by residual: angle pdb=" N HIS C 241 " pdb=" CA HIS C 241 " pdb=" CB HIS C 241 " ideal model delta sigma weight residual 114.27 108.67 5.60 1.64e+00 3.72e-01 1.17e+01 angle pdb=" C ARG C 239 " pdb=" N ALA C 240 " pdb=" CA ALA C 240 " ideal model delta sigma weight residual 122.16 125.63 -3.47 1.32e+00 5.74e-01 6.91e+00 angle pdb=" N LEU C 282 " pdb=" CA LEU C 282 " pdb=" CB LEU C 282 " ideal model delta sigma weight residual 113.65 110.06 3.59 1.47e+00 4.63e-01 5.97e+00 angle pdb=" C ALA C 240 " pdb=" N HIS C 241 " pdb=" CA HIS C 241 " ideal model delta sigma weight residual 125.66 121.96 3.70 1.85e+00 2.92e-01 4.01e+00 angle pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N HIS C 59 " ideal model delta sigma weight residual 116.60 119.10 -2.50 1.45e+00 4.76e-01 2.97e+00 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 3569 16.80 - 33.60: 152 33.60 - 50.39: 72 50.39 - 67.19: 32 67.19 - 83.99: 12 Dihedral angle restraints: 3837 sinusoidal: 2094 harmonic: 1743 Sorted by residual: dihedral pdb=" CA ALA C 240 " pdb=" C ALA C 240 " pdb=" N HIS C 241 " pdb=" CA HIS C 241 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR C 127 " pdb=" C TYR C 127 " pdb=" N GLY C 128 " pdb=" CA GLY C 128 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER C 238 " pdb=" C SER C 238 " pdb=" N ARG C 239 " pdb=" CA ARG C 239 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 418 0.026 - 0.052: 120 0.052 - 0.078: 55 0.078 - 0.104: 24 0.104 - 0.130: 12 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA VAL C 237 " pdb=" N VAL C 237 " pdb=" C VAL C 237 " pdb=" CB VAL C 237 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL C 45 " pdb=" N VAL C 45 " pdb=" C VAL C 45 " pdb=" CB VAL C 45 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 626 not shown) Planarity restraints: 1215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " -0.012 2.00e-02 2.50e+03 7.57e-03 1.72e+00 pdb=" CG PHE A 538 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 189 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO C 190 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 240 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C ALA C 240 " -0.018 2.00e-02 2.50e+03 pdb=" O ALA C 240 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS C 241 " 0.006 2.00e-02 2.50e+03 ... (remaining 1212 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 264 2.15 - 2.76: 15414 2.76 - 3.37: 23905 3.37 - 3.99: 30526 3.99 - 4.60: 48717 Nonbonded interactions: 118826 Sorted by model distance: nonbonded pdb=" HG SER C 120 " pdb=" OE2 GLU C 188 " model vdw 1.535 1.850 nonbonded pdb=" O VAL C 94 " pdb=" HG1 THR C 98 " model vdw 1.619 1.850 nonbonded pdb=" O GLY C 73 " pdb=" HH TYR C 80 " model vdw 1.619 1.850 nonbonded pdb=" O GLU A 565 " pdb=" HG1 THR A 568 " model vdw 1.637 1.850 nonbonded pdb=" OD1 ASP C 202 " pdb="HH21 ARG C 239 " model vdw 1.648 1.850 ... (remaining 118821 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: 15.480 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: 0.130 Extract box with map and model: 31.480 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 34.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.002 0.042 4156 Z= 0.141 Angle : 0.460 5.602 5633 Z= 0.255 Chirality : 0.036 0.130 629 Planarity : 0.003 0.030 728 Dihedral : 9.781 83.990 1539 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.67 % Allowed : 0.22 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.15 (0.38), residues: 504 helix: 1.17 (0.31), residues: 285 sheet: 0.20 (0.90), residues: 36 loop : 0.43 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 417 HIS 0.005 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.009 0.001 TYR C 127 ARG 0.002 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 GLN cc_start: 0.9177 (tt0) cc_final: 0.8851 (tt0) REVERT: A 555 THR cc_start: 0.9603 (m) cc_final: 0.9123 (p) REVERT: A 558 SER cc_start: 0.9482 (t) cc_final: 0.9222 (p) REVERT: C 197 ASP cc_start: 0.8834 (m-30) cc_final: 0.8421 (m-30) REVERT: C 238 SER cc_start: 0.9108 (t) cc_final: 0.8734 (p) outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 1.6937 time to fit residues: 155.0052 Evaluate side-chains 59 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.0010 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4156 Z= 0.263 Angle : 0.574 7.666 5633 Z= 0.304 Chirality : 0.039 0.132 629 Planarity : 0.004 0.057 728 Dihedral : 4.633 26.380 556 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.67 % Allowed : 9.17 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.19 (0.38), residues: 504 helix: 1.38 (0.31), residues: 293 sheet: 0.06 (0.92), residues: 37 loop : 0.10 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 417 HIS 0.004 0.001 HIS C 63 PHE 0.024 0.002 PHE A 538 TYR 0.010 0.001 TYR C 265 ARG 0.008 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8743 (m) cc_final: 0.8449 (p) REVERT: A 514 GLN cc_start: 0.9016 (tt0) cc_final: 0.8646 (tt0) REVERT: A 517 THR cc_start: 0.9519 (m) cc_final: 0.9187 (p) REVERT: A 558 SER cc_start: 0.9496 (t) cc_final: 0.9212 (p) REVERT: C 238 SER cc_start: 0.9071 (t) cc_final: 0.8658 (p) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 1.8751 time to fit residues: 116.1416 Evaluate side-chains 53 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain C residue 57 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.0050 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4156 Z= 0.177 Angle : 0.506 5.930 5633 Z= 0.266 Chirality : 0.037 0.128 629 Planarity : 0.003 0.027 728 Dihedral : 4.159 19.586 554 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.48 (0.38), residues: 504 helix: 1.59 (0.31), residues: 299 sheet: -0.01 (0.90), residues: 37 loop : 0.27 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 PHE 0.021 0.001 PHE A 538 TYR 0.007 0.001 TYR C 265 ARG 0.003 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASN cc_start: 0.8797 (t0) cc_final: 0.8369 (t0) REVERT: A 512 CYS cc_start: 0.8724 (m) cc_final: 0.8447 (p) REVERT: A 517 THR cc_start: 0.9513 (m) cc_final: 0.9235 (p) REVERT: A 558 SER cc_start: 0.9530 (t) cc_final: 0.9245 (p) REVERT: C 119 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8037 (mm-30) REVERT: C 238 SER cc_start: 0.9121 (t) cc_final: 0.8765 (p) REVERT: D 98 ASN cc_start: 0.6758 (p0) cc_final: 0.6553 (p0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 2.0085 time to fit residues: 117.8083 Evaluate side-chains 51 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4156 Z= 0.207 Angle : 0.501 5.572 5633 Z= 0.264 Chirality : 0.037 0.132 629 Planarity : 0.004 0.055 728 Dihedral : 4.055 18.978 554 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.22 % Allowed : 11.41 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.38), residues: 504 helix: 1.65 (0.31), residues: 299 sheet: -0.01 (0.88), residues: 37 loop : 0.19 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.007 0.001 TYR C 265 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASN cc_start: 0.8782 (t0) cc_final: 0.8473 (t0) REVERT: A 512 CYS cc_start: 0.8765 (m) cc_final: 0.8491 (p) REVERT: A 517 THR cc_start: 0.9492 (m) cc_final: 0.9245 (p) REVERT: A 558 SER cc_start: 0.9543 (t) cc_final: 0.9264 (p) REVERT: C 238 SER cc_start: 0.9127 (t) cc_final: 0.8784 (p) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 2.0616 time to fit residues: 116.5604 Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4156 Z= 0.245 Angle : 0.497 4.823 5633 Z= 0.264 Chirality : 0.038 0.134 629 Planarity : 0.004 0.047 728 Dihedral : 4.028 18.568 554 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.89 % Allowed : 12.30 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.46 (0.39), residues: 504 helix: 1.61 (0.31), residues: 301 sheet: -0.07 (0.87), residues: 37 loop : 0.18 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.007 0.001 TYR C 265 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASN cc_start: 0.8788 (t0) cc_final: 0.8572 (t0) REVERT: A 558 SER cc_start: 0.9553 (t) cc_final: 0.9264 (p) REVERT: C 238 SER cc_start: 0.9172 (t) cc_final: 0.8836 (p) REVERT: C 242 GLN cc_start: 0.8763 (tt0) cc_final: 0.8418 (tt0) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 2.1539 time to fit residues: 112.4241 Evaluate side-chains 48 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 552 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4156 Z= 0.161 Angle : 0.469 4.640 5633 Z= 0.247 Chirality : 0.037 0.128 629 Planarity : 0.004 0.051 728 Dihedral : 3.881 18.212 554 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.64 (0.39), residues: 504 helix: 1.77 (0.31), residues: 299 sheet: -0.06 (0.85), residues: 37 loop : 0.25 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 417 HIS 0.003 0.000 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.005 0.001 TYR C 265 ARG 0.006 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8800 (m) cc_final: 0.8505 (p) REVERT: A 558 SER cc_start: 0.9555 (t) cc_final: 0.9265 (p) REVERT: C 238 SER cc_start: 0.9171 (t) cc_final: 0.8859 (p) REVERT: C 242 GLN cc_start: 0.8734 (tt0) cc_final: 0.8343 (tt0) outliers start: 0 outliers final: 1 residues processed: 47 average time/residue: 2.2284 time to fit residues: 109.4243 Evaluate side-chains 47 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4156 Z= 0.202 Angle : 0.481 4.477 5633 Z= 0.254 Chirality : 0.037 0.132 629 Planarity : 0.004 0.052 728 Dihedral : 3.858 17.891 554 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.45 % Allowed : 13.65 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.66 (0.39), residues: 504 helix: 1.74 (0.31), residues: 301 sheet: 0.02 (0.86), residues: 37 loop : 0.30 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.005 0.001 TYR C 265 ARG 0.006 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8762 (m) cc_final: 0.8472 (p) REVERT: A 558 SER cc_start: 0.9557 (t) cc_final: 0.9267 (p) REVERT: C 238 SER cc_start: 0.9170 (t) cc_final: 0.8856 (p) REVERT: C 242 GLN cc_start: 0.8718 (tt0) cc_final: 0.8241 (tt0) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 2.2470 time to fit residues: 115.7676 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4156 Z= 0.195 Angle : 0.479 4.472 5633 Z= 0.252 Chirality : 0.037 0.131 629 Planarity : 0.004 0.054 728 Dihedral : 3.836 17.757 554 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.22 % Allowed : 13.65 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.39), residues: 504 helix: 1.80 (0.31), residues: 301 sheet: 0.08 (0.86), residues: 37 loop : 0.27 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.005 0.001 TYR A 495 ARG 0.008 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8789 (m) cc_final: 0.8502 (p) REVERT: A 558 SER cc_start: 0.9558 (t) cc_final: 0.9270 (p) REVERT: C 238 SER cc_start: 0.9169 (t) cc_final: 0.8861 (p) REVERT: C 242 GLN cc_start: 0.8698 (tt0) cc_final: 0.8371 (tt0) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 2.2066 time to fit residues: 103.5837 Evaluate side-chains 45 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4156 Z= 0.199 Angle : 0.491 5.351 5633 Z= 0.257 Chirality : 0.037 0.130 629 Planarity : 0.004 0.055 728 Dihedral : 3.818 17.573 554 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.74 (0.39), residues: 504 helix: 1.83 (0.31), residues: 301 sheet: 0.09 (0.86), residues: 37 loop : 0.29 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.000 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.005 0.001 TYR A 495 ARG 0.007 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8778 (m) cc_final: 0.8490 (p) REVERT: A 558 SER cc_start: 0.9559 (t) cc_final: 0.9270 (p) REVERT: C 238 SER cc_start: 0.9175 (t) cc_final: 0.8879 (p) REVERT: C 242 GLN cc_start: 0.8687 (tt0) cc_final: 0.8360 (tt0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 2.2861 time to fit residues: 109.9256 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4156 Z= 0.190 Angle : 0.482 5.329 5633 Z= 0.253 Chirality : 0.037 0.129 629 Planarity : 0.004 0.056 728 Dihedral : 3.795 17.422 554 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.45 % Allowed : 13.20 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.77 (0.39), residues: 504 helix: 1.86 (0.31), residues: 301 sheet: 0.06 (0.86), residues: 37 loop : 0.27 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.006 0.001 TYR C 152 ARG 0.007 0.000 ARG A 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8775 (m) cc_final: 0.8484 (p) REVERT: A 558 SER cc_start: 0.9559 (t) cc_final: 0.9270 (p) REVERT: C 238 SER cc_start: 0.9166 (t) cc_final: 0.8875 (p) REVERT: C 242 GLN cc_start: 0.8677 (tt0) cc_final: 0.8354 (tt0) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 2.0807 time to fit residues: 106.7077 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053582 restraints weight = 30998.220| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.43 r_work: 0.2754 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4156 Z= 0.188 Angle : 0.501 6.616 5633 Z= 0.258 Chirality : 0.037 0.128 629 Planarity : 0.004 0.056 728 Dihedral : 3.765 17.309 554 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 13.87 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.82 (0.39), residues: 504 helix: 1.91 (0.31), residues: 301 sheet: 0.09 (0.86), residues: 37 loop : 0.29 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.000 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.005 0.001 TYR A 495 ARG 0.007 0.000 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4361.09 seconds wall clock time: 79 minutes 5.44 seconds (4745.44 seconds total)