Starting phenix.real_space_refine on Fri Dec 8 10:01:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/12_2023/8twi_41668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/12_2023/8twi_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_41668/12_2023/8twi_41668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/12_2023/8twi_41668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/12_2023/8twi_41668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/12_2023/8twi_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-1.21rc1-5172/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: 4.22, 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: 7.04 Conformation dependent library (CDL) restraints added in 841.1 milliseconds 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: 0.68 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: 3.05 Time building geometry restraints manager: 7.15 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: 3520 16.80 - 33.60: 136 33.60 - 50.39: 49 50.39 - 67.19: 21 67.19 - 83.99: 12 Dihedral angle restraints: 3738 sinusoidal: 1995 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 3735 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: 11.290 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: 31.490 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 33.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.140 ------------------------------------------------------------------------------- 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 : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 1.6838 time to fit residues: 154.1712 Evaluate side-chains 55 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2369 time to fit residues: 1.1621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4156 Z= 0.262 Angle : 0.572 7.792 5633 Z= 0.303 Chirality : 0.039 0.136 629 Planarity : 0.004 0.056 728 Dihedral : 4.513 20.344 554 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.89 % Allowed : 10.74 % 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: 1.31 (0.38), residues: 504 helix: 1.42 (0.31), residues: 298 sheet: 0.03 (0.92), residues: 37 loop : 0.25 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 PHE 0.023 0.001 PHE A 538 TYR 0.010 0.001 TYR C 265 ARG 0.005 0.000 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 57 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 1.9079 time to fit residues: 114.3334 Evaluate side-chains 48 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.9245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 37 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4156 Z= 0.173 Angle : 0.517 5.879 5633 Z= 0.271 Chirality : 0.037 0.129 629 Planarity : 0.003 0.028 728 Dihedral : 4.233 19.305 554 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.45 % Allowed : 11.41 % Favored : 88.14 % 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: 1.44 (0.38), residues: 504 helix: 1.57 (0.31), residues: 299 sheet: -0.06 (0.90), residues: 37 loop : 0.24 (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 0.022 0.001 PHE A 538 TYR 0.008 0.001 TYR C 265 ARG 0.002 0.000 ARG C 49 *********************** 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: 2 poor density : 54 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 2.0380 time to fit residues: 119.6613 Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.9600 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4156 Z= 0.274 Angle : 0.531 5.662 5633 Z= 0.283 Chirality : 0.039 0.138 629 Planarity : 0.004 0.055 728 Dihedral : 4.255 18.924 554 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.67 % Allowed : 13.42 % 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: 1.37 (0.39), residues: 504 helix: 1.54 (0.31), residues: 300 sheet: -0.09 (0.90), residues: 37 loop : 0.12 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 417 HIS 0.004 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 50 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 2.1822 time to fit residues: 111.8145 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1604 time to fit residues: 0.9900 ------------------------------------------------------------------------------- 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: 0.1980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4156 Z= 0.184 Angle : 0.499 5.064 5633 Z= 0.264 Chirality : 0.037 0.129 629 Planarity : 0.003 0.046 728 Dihedral : 4.085 18.463 554 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.12 % Allowed : 13.65 % Favored : 85.23 % 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: 1.53 (0.39), residues: 504 helix: 1.68 (0.31), residues: 300 sheet: -0.12 (0.88), residues: 37 loop : 0.19 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 417 HIS 0.002 0.001 HIS C 241 PHE 0.023 0.001 PHE A 538 TYR 0.006 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 50 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 2.1713 time to fit residues: 109.1169 Evaluate side-chains 45 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.8606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.3610 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= 0.168 Angle : 0.477 4.766 5633 Z= 0.253 Chirality : 0.037 0.129 629 Planarity : 0.004 0.051 728 Dihedral : 3.982 18.170 554 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.89 % Allowed : 13.87 % Favored : 85.23 % 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: 1.63 (0.39), residues: 504 helix: 1.74 (0.31), residues: 301 sheet: -0.04 (0.87), residues: 37 loop : 0.25 (0.51), 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 0.005 0.001 TYR A 495 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: 4 poor density : 43 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 46 average time/residue: 2.1693 time to fit residues: 104.4715 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.7963 time to fit residues: 2.5954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.3737 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= 0.181 Angle : 0.486 4.507 5633 Z= 0.258 Chirality : 0.037 0.131 629 Planarity : 0.004 0.050 728 Dihedral : 3.929 17.901 554 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.12 % Allowed : 14.09 % Favored : 84.79 % 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: 1.67 (0.39), residues: 504 helix: 1.77 (0.31), residues: 302 sheet: 0.03 (0.87), residues: 37 loop : 0.26 (0.51), residues: 165 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 0.006 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 48 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 2.0495 time to fit residues: 99.1883 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.7809 time to fit residues: 2.5683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.3804 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= 0.182 Angle : 0.480 4.656 5633 Z= 0.254 Chirality : 0.037 0.130 629 Planarity : 0.004 0.053 728 Dihedral : 3.910 17.685 554 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 14.32 % Favored : 84.79 % 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: 1.73 (0.39), residues: 504 helix: 1.83 (0.31), residues: 302 sheet: 0.04 (0.86), residues: 37 loop : 0.25 (0.51), residues: 165 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 0.005 0.001 TYR A 495 ARG 0.006 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: 4 poor density : 42 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 5 residues processed: 45 average time/residue: 2.1291 time to fit residues: 100.7059 Evaluate side-chains 47 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 2 average time/residue: 0.2138 time to fit residues: 1.4651 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8147 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4156 Z= 0.185 Angle : 0.488 4.568 5633 Z= 0.258 Chirality : 0.037 0.129 629 Planarity : 0.004 0.055 728 Dihedral : 3.880 17.518 554 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 14.32 % Favored : 84.79 % 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: 1.76 (0.39), residues: 504 helix: 1.86 (0.31), residues: 302 sheet: 0.07 (0.85), residues: 37 loop : 0.25 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 477 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 0.007 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: 4 poor density : 42 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 2.1427 time to fit residues: 100.9546 Evaluate side-chains 44 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1715 time to fit residues: 1.1619 ------------------------------------------------------------------------------- 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: 0.7980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8159 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4156 Z= 0.240 Angle : 0.499 4.659 5633 Z= 0.267 Chirality : 0.038 0.132 629 Planarity : 0.004 0.056 728 Dihedral : 3.947 17.575 554 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.45 % Allowed : 14.77 % Favored : 84.79 % 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: 1.76 (0.31), residues: 302 sheet: 0.05 (0.84), residues: 37 loop : 0.19 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.007 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 45 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 4 residues processed: 45 average time/residue: 2.1490 time to fit residues: 101.3666 Evaluate side-chains 45 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 2 average time/residue: 0.2404 time to fit residues: 1.4744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.074828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053296 restraints weight = 30610.593| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.47 r_work: 0.2749 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4027 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= 0.187 Angle : 0.495 5.129 5633 Z= 0.262 Chirality : 0.037 0.128 629 Planarity : 0.004 0.054 728 Dihedral : 3.892 17.521 554 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.12 % Allowed : 14.54 % Favored : 84.34 % 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: 1.72 (0.39), residues: 504 helix: 1.82 (0.31), residues: 302 sheet: 0.09 (0.86), residues: 37 loop : 0.25 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 477 HIS 0.003 0.001 HIS C 63 PHE 0.022 0.001 PHE A 538 TYR 0.007 0.001 TYR C 86 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: 4198.00 seconds wall clock time: 74 minutes 47.43 seconds (4487.43 seconds total)