Starting phenix.real_space_refine on Sun Mar 10 21:21:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/03_2024/7slp_25197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/03_2024/7slp_25197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/03_2024/7slp_25197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/03_2024/7slp_25197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/03_2024/7slp_25197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/03_2024/7slp_25197_updated.pdb" } resolution = 4.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 15 5.16 5 C 3151 2.51 5 N 912 2.21 5 O 1061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ASP 593": "OD1" <-> "OD2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 565": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1887 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2481 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 782 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 12, 'rna3p': 24} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.76 Number of scatterers: 5176 At special positions: 0 Unit cell: (81.32, 78.11, 101.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 37 15.00 O 1061 8.00 N 912 7.00 C 3151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 970.0 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 3 sheets defined 42.4% alpha, 9.3% beta 8 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 433 through 436 No H-bonds generated for 'chain 'A' and resid 433 through 436' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.035A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 594 through 606 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.582A pdb=" N THR A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 122 through 125 No H-bonds generated for 'chain 'B' and resid 122 through 125' Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.502A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 412 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.967A pdb=" N ILE B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 553 through 570 Processing sheet with id= A, first strand: chain 'A' and resid 660 through 662 removed outlier: 3.528A pdb=" N CYS A 580 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 616 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 581 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 554 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP A 474 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 556 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.749A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 519 through 523 167 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1067 1.33 - 1.45: 1463 1.45 - 1.57: 2736 1.57 - 1.70: 73 1.70 - 1.82: 21 Bond restraints: 5360 Sorted by residual: bond pdb=" N GLU A 574 " pdb=" CA GLU A 574 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.22e+00 bond pdb=" C2 SAH A 701 " pdb=" N3 SAH A 701 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" N LYS A 625 " pdb=" CA LYS A 625 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.37e+00 bond pdb=" N SER A 622 " pdb=" CA SER A 622 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N LYS B 112 " pdb=" CA LYS B 112 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.23e+00 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 93.07 - 101.29: 21 101.29 - 109.52: 1077 109.52 - 117.74: 3128 117.74 - 125.97: 3014 125.97 - 134.19: 196 Bond angle restraints: 7436 Sorted by residual: angle pdb=" N LEU B 131 " pdb=" CA LEU B 131 " pdb=" C LEU B 131 " ideal model delta sigma weight residual 110.91 120.44 -9.53 1.17e+00 7.31e-01 6.64e+01 angle pdb=" C PRO A 573 " pdb=" CA PRO A 573 " pdb=" CB PRO A 573 " ideal model delta sigma weight residual 111.11 102.94 8.17 1.17e+00 7.31e-01 4.88e+01 angle pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 119.08 -9.68 1.50e+00 4.44e-01 4.16e+01 angle pdb=" N GLU B 480 " pdb=" CA GLU B 480 " pdb=" C GLU B 480 " ideal model delta sigma weight residual 109.15 118.31 -9.16 1.44e+00 4.82e-01 4.05e+01 angle pdb=" C SER B 479 " pdb=" CA SER B 479 " pdb=" CB SER B 479 " ideal model delta sigma weight residual 112.78 101.99 10.79 2.18e+00 2.10e-01 2.45e+01 ... (remaining 7431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 2895 21.54 - 43.07: 262 43.07 - 64.60: 88 64.60 - 86.14: 24 86.14 - 107.67: 7 Dihedral angle restraints: 3276 sinusoidal: 1641 harmonic: 1635 Sorted by residual: dihedral pdb=" CA ASN A 426 " pdb=" C ASN A 426 " pdb=" N PRO A 427 " pdb=" CA PRO A 427 " ideal model delta harmonic sigma weight residual 180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N LYS A 683 " pdb=" CA LYS A 683 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ARG B 55 " pdb=" C ARG B 55 " pdb=" N PHE B 56 " pdb=" CA PHE B 56 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 3273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 733 0.086 - 0.173: 115 0.173 - 0.259: 16 0.259 - 0.345: 1 0.345 - 0.432: 2 Chirality restraints: 867 Sorted by residual: chirality pdb=" CB VAL B 99 " pdb=" CA VAL B 99 " pdb=" CG1 VAL B 99 " pdb=" CG2 VAL B 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA PHE A 523 " pdb=" N PHE A 523 " pdb=" C PHE A 523 " pdb=" CB PHE A 523 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA LEU B 131 " pdb=" N LEU B 131 " pdb=" C LEU B 131 " pdb=" CB LEU B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 864 not shown) Planarity restraints: 807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 643 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 644 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 539 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C VAL A 539 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 539 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO A 540 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 588 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C HIS A 588 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS A 588 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 589 " 0.014 2.00e-02 2.50e+03 ... (remaining 804 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 817 2.76 - 3.29: 4655 3.29 - 3.83: 9056 3.83 - 4.36: 9885 4.36 - 4.90: 15915 Nonbonded interactions: 40328 Sorted by model distance: nonbonded pdb=" O2' C R 320 " pdb=" OP1 C R 323 " model vdw 2.221 2.440 nonbonded pdb=" O2' U R 327 " pdb=" O2 U R 327 " model vdw 2.233 2.440 nonbonded pdb=" O GLN B 470 " pdb=" OG1 THR B 474 " model vdw 2.298 2.440 nonbonded pdb=" NH2 ARG B 552 " pdb=" N7 G R 303 " model vdw 2.303 2.600 nonbonded pdb=" O ARG A 425 " pdb=" OH TYR A 490 " model vdw 2.306 2.440 ... (remaining 40323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.000 Extract box with map and model: 2.020 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 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 : 0.008 0.100 5360 Z= 0.525 Angle : 1.220 10.794 7436 Z= 0.688 Chirality : 0.067 0.432 867 Planarity : 0.008 0.065 807 Dihedral : 19.399 107.672 2218 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.20 % Favored : 95.26 % Rotamer: Outliers : 1.77 % Allowed : 9.49 % Favored : 88.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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: -3.76 (0.27), residues: 548 helix: -3.01 (0.21), residues: 266 sheet: 0.07 (0.64), residues: 60 loop : -2.38 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 384 HIS 0.009 0.003 HIS B 494 PHE 0.033 0.004 PHE A 442 TYR 0.029 0.005 TYR A 661 ARG 0.010 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.7271 (ttt) cc_final: 0.6914 (tmm) REVERT: A 538 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7808 (mt0) REVERT: A 557 THR cc_start: 0.6231 (t) cc_final: 0.5925 (t) REVERT: A 582 SER cc_start: 0.6965 (m) cc_final: 0.6745 (t) REVERT: A 607 LEU cc_start: 0.5854 (mt) cc_final: 0.5630 (mp) REVERT: A 661 TYR cc_start: 0.6298 (p90) cc_final: 0.6022 (p90) REVERT: B 50 ASN cc_start: 0.7391 (t0) cc_final: 0.7135 (t0) REVERT: B 123 ASP cc_start: 0.8371 (t0) cc_final: 0.8167 (t0) REVERT: B 159 TYR cc_start: 0.6892 (m-80) cc_final: 0.6437 (m-80) REVERT: B 459 ILE cc_start: 0.7413 (mt) cc_final: 0.7138 (tt) outliers start: 8 outliers final: 4 residues processed: 158 average time/residue: 0.1906 time to fit residues: 37.4326 Evaluate side-chains 89 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN B 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5360 Z= 0.201 Angle : 0.642 7.715 7436 Z= 0.325 Chirality : 0.038 0.140 867 Planarity : 0.006 0.077 807 Dihedral : 19.326 101.076 1201 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.93 (0.31), residues: 548 helix: -1.01 (0.29), residues: 262 sheet: -0.15 (0.70), residues: 50 loop : -1.75 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 586 HIS 0.006 0.002 HIS A 588 PHE 0.012 0.002 PHE B 44 TYR 0.014 0.002 TYR A 650 ARG 0.005 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 CYS cc_start: 0.8542 (p) cc_final: 0.7763 (p) REVERT: A 538 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8373 (mt0) REVERT: A 582 SER cc_start: 0.7352 (m) cc_final: 0.6864 (t) REVERT: A 630 THR cc_start: 0.7059 (p) cc_final: 0.6645 (t) REVERT: B 50 ASN cc_start: 0.7595 (t0) cc_final: 0.7189 (t0) REVERT: B 77 PHE cc_start: 0.7924 (m-10) cc_final: 0.7706 (m-80) REVERT: B 383 GLU cc_start: 0.8048 (tt0) cc_final: 0.7741 (tt0) REVERT: B 408 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6367 (mt0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1953 time to fit residues: 28.4590 Evaluate side-chains 77 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.8244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5360 Z= 0.275 Angle : 0.743 8.616 7436 Z= 0.378 Chirality : 0.041 0.139 867 Planarity : 0.007 0.097 807 Dihedral : 19.291 103.081 1201 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.33), residues: 548 helix: -0.54 (0.30), residues: 253 sheet: 0.61 (0.64), residues: 64 loop : -1.86 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 519 HIS 0.009 0.002 HIS A 606 PHE 0.029 0.003 PHE A 523 TYR 0.019 0.002 TYR A 490 ARG 0.007 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.6752 (tpp) cc_final: 0.5835 (tpt) REVERT: B 154 ILE cc_start: 0.8382 (mt) cc_final: 0.8182 (mp) REVERT: B 184 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 390 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8430 (tm-30) REVERT: B 401 SER cc_start: 0.8959 (m) cc_final: 0.8525 (p) REVERT: B 540 ARG cc_start: 0.6654 (ppt170) cc_final: 0.6209 (ptm160) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1661 time to fit residues: 23.0043 Evaluate side-chains 76 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 456 HIS ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 1.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 5360 Z= 0.451 Angle : 0.903 9.186 7436 Z= 0.463 Chirality : 0.047 0.188 867 Planarity : 0.007 0.087 807 Dihedral : 20.003 98.683 1201 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.81 (0.33), residues: 548 helix: -0.89 (0.29), residues: 251 sheet: 0.08 (0.62), residues: 67 loop : -1.87 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 519 HIS 0.009 0.003 HIS B 517 PHE 0.030 0.003 PHE B 44 TYR 0.018 0.003 TYR B 532 ARG 0.005 0.001 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 401 SER cc_start: 0.9044 (m) cc_final: 0.8676 (p) REVERT: B 540 ARG cc_start: 0.7198 (ppt170) cc_final: 0.6897 (ptm160) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1625 time to fit residues: 17.5824 Evaluate side-chains 59 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 1.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5360 Z= 0.162 Angle : 0.578 5.760 7436 Z= 0.292 Chirality : 0.038 0.135 867 Planarity : 0.005 0.083 807 Dihedral : 18.916 91.048 1201 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.00 (0.34), residues: 548 helix: 0.08 (0.31), residues: 254 sheet: 0.09 (0.63), residues: 65 loop : -1.71 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 519 HIS 0.006 0.001 HIS A 606 PHE 0.011 0.001 PHE A 523 TYR 0.018 0.002 TYR A 661 ARG 0.002 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 596 LEU cc_start: 0.8428 (tp) cc_final: 0.8219 (tp) REVERT: A 614 VAL cc_start: 0.8784 (t) cc_final: 0.8580 (m) REVERT: B 42 VAL cc_start: 0.9256 (t) cc_final: 0.9004 (p) REVERT: B 390 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 401 SER cc_start: 0.9002 (m) cc_final: 0.8636 (p) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1671 time to fit residues: 18.8106 Evaluate side-chains 66 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 0.0020 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 1.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5360 Z= 0.259 Angle : 0.660 6.454 7436 Z= 0.332 Chirality : 0.039 0.134 867 Planarity : 0.005 0.084 807 Dihedral : 19.100 95.351 1201 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.34), residues: 548 helix: 0.19 (0.31), residues: 254 sheet: 0.29 (0.65), residues: 65 loop : -1.82 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 384 HIS 0.008 0.002 HIS A 606 PHE 0.014 0.002 PHE B 77 TYR 0.018 0.002 TYR A 604 ARG 0.004 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.6655 (t70) cc_final: 0.6387 (t70) REVERT: A 623 TYR cc_start: 0.6158 (m-10) cc_final: 0.5830 (m-10) REVERT: A 662 GLU cc_start: 0.5628 (pt0) cc_final: 0.4851 (pp20) REVERT: B 390 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 401 SER cc_start: 0.8883 (m) cc_final: 0.8664 (p) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1429 time to fit residues: 15.6140 Evaluate side-chains 64 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.0010 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 1.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5360 Z= 0.138 Angle : 0.551 7.549 7436 Z= 0.272 Chirality : 0.036 0.132 867 Planarity : 0.005 0.088 807 Dihedral : 18.647 94.518 1201 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.35), residues: 548 helix: 0.66 (0.32), residues: 255 sheet: 0.56 (0.67), residues: 62 loop : -1.81 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 519 HIS 0.006 0.001 HIS A 489 PHE 0.014 0.001 PHE B 185 TYR 0.017 0.001 TYR A 661 ARG 0.002 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.9419 (tp) cc_final: 0.9085 (tt) REVERT: A 575 TYR cc_start: 0.8174 (m-80) cc_final: 0.7905 (m-80) REVERT: B 123 ASP cc_start: 0.8698 (t70) cc_final: 0.8488 (t0) REVERT: B 390 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1711 time to fit residues: 17.9609 Evaluate side-chains 60 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 1.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5360 Z= 0.185 Angle : 0.589 6.742 7436 Z= 0.291 Chirality : 0.037 0.135 867 Planarity : 0.005 0.082 807 Dihedral : 18.671 94.924 1201 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.35), residues: 548 helix: 0.76 (0.33), residues: 255 sheet: 0.70 (0.68), residues: 62 loop : -1.82 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 586 HIS 0.005 0.002 HIS A 606 PHE 0.011 0.002 PHE B 185 TYR 0.014 0.002 TYR B 391 ARG 0.002 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 579 LEU cc_start: 0.8237 (tp) cc_final: 0.8001 (tp) REVERT: A 586 TRP cc_start: 0.7184 (m100) cc_final: 0.6830 (m100) REVERT: B 390 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8123 (tm-30) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1238 time to fit residues: 13.6499 Evaluate side-chains 58 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 1.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5360 Z= 0.181 Angle : 0.582 7.981 7436 Z= 0.289 Chirality : 0.037 0.136 867 Planarity : 0.005 0.077 807 Dihedral : 18.626 94.988 1201 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.36), residues: 548 helix: 0.90 (0.33), residues: 255 sheet: 0.78 (0.68), residues: 62 loop : -1.78 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 586 HIS 0.005 0.001 HIS A 588 PHE 0.011 0.001 PHE B 185 TYR 0.024 0.002 TYR A 623 ARG 0.002 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LEU cc_start: 0.8164 (tp) cc_final: 0.7848 (tp) REVERT: A 586 TRP cc_start: 0.7191 (m100) cc_final: 0.6792 (m100) REVERT: B 84 THR cc_start: 0.7081 (m) cc_final: 0.6682 (m) REVERT: B 390 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 540 ARG cc_start: 0.6384 (tmt170) cc_final: 0.5641 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1294 time to fit residues: 13.6100 Evaluate side-chains 58 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.0030 chunk 28 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN A 606 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 1.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5360 Z= 0.135 Angle : 0.553 8.319 7436 Z= 0.272 Chirality : 0.037 0.129 867 Planarity : 0.005 0.079 807 Dihedral : 18.361 94.406 1201 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.36), residues: 548 helix: 1.08 (0.33), residues: 254 sheet: 1.06 (0.66), residues: 60 loop : -1.74 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 586 HIS 0.004 0.001 HIS A 489 PHE 0.012 0.001 PHE B 185 TYR 0.016 0.001 TYR A 623 ARG 0.002 0.000 ARG B 548 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 579 LEU cc_start: 0.8262 (tp) cc_final: 0.7897 (tp) REVERT: A 586 TRP cc_start: 0.7036 (m100) cc_final: 0.6760 (m100) REVERT: B 540 ARG cc_start: 0.6472 (tmt170) cc_final: 0.5767 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1374 time to fit residues: 14.3736 Evaluate side-chains 61 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.151007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.128908 restraints weight = 12605.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129581 restraints weight = 10019.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131235 restraints weight = 8308.916| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 1.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5360 Z= 0.142 Angle : 0.559 8.544 7436 Z= 0.269 Chirality : 0.037 0.148 867 Planarity : 0.005 0.080 807 Dihedral : 18.200 93.903 1201 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.36), residues: 548 helix: 1.20 (0.34), residues: 254 sheet: 1.33 (0.67), residues: 60 loop : -1.63 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 586 HIS 0.009 0.002 HIS A 606 PHE 0.011 0.001 PHE B 185 TYR 0.014 0.001 TYR B 391 ARG 0.002 0.000 ARG B 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.01 seconds wall clock time: 24 minutes 52.39 seconds (1492.39 seconds total)