Starting phenix.real_space_refine (version: dev) on Sun Dec 11 16:21:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2022/7slp_25197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2022/7slp_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_25197/12_2022/7slp_25197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2022/7slp_25197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2022/7slp_25197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2022/7slp_25197_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 3.78, per 1000 atoms: 0.73 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: 2.49 Conformation dependent library (CDL) restraints added in 671.0 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: 1.76 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: 1.65 Time building geometry restraints manager: 2.60 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: 2833 21.54 - 43.07: 231 43.07 - 64.60: 48 64.60 - 86.14: 13 86.14 - 107.67: 7 Dihedral angle restraints: 3132 sinusoidal: 1497 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 3129 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 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. 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.180 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 20.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 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 : 17.077 107.672 2074 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.20 % Favored : 95.26 % Rotamer Outliers : 1.77 % 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 *********************** 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 : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 158 average time/residue: 0.1825 time to fit residues: 36.0492 Evaluate side-chains 85 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0570 time to fit residues: 1.1543 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5360 Z= 0.220 Angle : 0.664 7.316 7436 Z= 0.336 Chirality : 0.039 0.257 867 Planarity : 0.007 0.082 807 Dihedral : 14.579 101.415 1057 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % 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: -1.88 (0.32), residues: 548 helix: -0.95 (0.29), residues: 262 sheet: 0.06 (0.65), residues: 59 loop : -1.87 (0.34), residues: 227 *********************** 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 109 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1829 time to fit residues: 25.5082 Evaluate side-chains 70 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7830 ------------------------------------------------------------------------------- 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: 0.0770 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5360 Z= 0.164 Angle : 0.579 6.376 7436 Z= 0.293 Chirality : 0.037 0.209 867 Planarity : 0.006 0.101 807 Dihedral : 13.913 105.059 1057 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.00 % 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: -0.93 (0.34), residues: 548 helix: -0.14 (0.31), residues: 255 sheet: 0.61 (0.75), residues: 50 loop : -1.35 (0.36), residues: 243 *********************** 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 102 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1552 time to fit residues: 20.9175 Evaluate side-chains 76 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7527 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 408 GLN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.9933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 5360 Z= 0.346 Angle : 0.818 8.597 7436 Z= 0.413 Chirality : 0.045 0.190 867 Planarity : 0.007 0.097 807 Dihedral : 15.040 100.196 1057 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.22 % 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: -1.63 (0.33), residues: 548 helix: -0.69 (0.29), residues: 252 sheet: -0.54 (0.71), residues: 52 loop : -1.54 (0.38), residues: 244 *********************** 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 91 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.1494 time to fit residues: 18.2491 Evaluate side-chains 68 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0672 time to fit residues: 0.9211 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A 606 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 1.0410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5360 Z= 0.193 Angle : 0.597 6.496 7436 Z= 0.303 Chirality : 0.038 0.167 867 Planarity : 0.005 0.083 807 Dihedral : 13.957 96.357 1057 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.00 % 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: -0.92 (0.34), residues: 548 helix: 0.16 (0.31), residues: 253 sheet: 0.22 (0.80), residues: 43 loop : -1.54 (0.36), residues: 252 *********************** 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 91 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1684 time to fit residues: 19.9958 Evaluate side-chains 65 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7655 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 481 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** B 408 GLN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 1.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 5360 Z= 0.239 Angle : 0.655 7.161 7436 Z= 0.329 Chirality : 0.040 0.180 867 Planarity : 0.006 0.100 807 Dihedral : 13.942 95.228 1057 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.22 % 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: -0.81 (0.34), residues: 548 helix: 0.29 (0.32), residues: 253 sheet: 0.49 (0.83), residues: 42 loop : -1.57 (0.37), residues: 253 *********************** 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 78 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1514 time to fit residues: 15.8515 Evaluate side-chains 61 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7673 ------------------------------------------------------------------------------- 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: 0.1980 chunk 47 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 HIS A 606 HIS B 408 GLN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 1.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5360 Z= 0.172 Angle : 0.591 7.728 7436 Z= 0.296 Chirality : 0.038 0.183 867 Planarity : 0.006 0.090 807 Dihedral : 13.475 94.775 1057 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.00 % 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: -0.49 (0.35), residues: 548 helix: 0.64 (0.33), residues: 253 sheet: 0.74 (0.85), residues: 42 loop : -1.54 (0.37), residues: 253 *********************** 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 71 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1492 time to fit residues: 14.4901 Evaluate side-chains 58 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7238 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 1.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 5360 Z= 0.331 Angle : 0.737 7.995 7436 Z= 0.374 Chirality : 0.042 0.183 867 Planarity : 0.006 0.093 807 Dihedral : 14.271 97.129 1057 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: -0.89 (0.35), residues: 548 helix: 0.20 (0.31), residues: 255 sheet: 0.10 (0.80), residues: 47 loop : -1.57 (0.39), residues: 246 *********************** 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 71 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.591 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1365 time to fit residues: 13.6173 Evaluate side-chains 56 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7621 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 606 HIS B 41 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 1.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 5360 Z= 0.250 Angle : 0.649 6.935 7436 Z= 0.326 Chirality : 0.040 0.175 867 Planarity : 0.006 0.084 807 Dihedral : 13.973 96.782 1057 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.00 % 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: -0.71 (0.36), residues: 548 helix: 0.40 (0.33), residues: 254 sheet: 0.34 (0.85), residues: 44 loop : -1.55 (0.38), residues: 250 *********************** 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 76 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1390 time to fit residues: 14.6205 Evaluate side-chains 56 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6751 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 46 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 HIS B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 1.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 5360 Z= 0.140 Angle : 0.588 7.602 7436 Z= 0.290 Chirality : 0.037 0.161 867 Planarity : 0.005 0.085 807 Dihedral : 13.047 94.728 1057 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.00 % 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 (0.34), residues: 245 sheet: 0.22 (0.84), residues: 46 loop : -1.38 (0.36), residues: 257 ********************** 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 79 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.587 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1289 time to fit residues: 14.3601 Evaluate side-chains 61 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8186 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 0.3980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 HIS A 606 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.151212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126597 restraints weight = 12553.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.128820 restraints weight = 9013.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130377 restraints weight = 7107.754| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 1.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 5360 Z= 0.173 Angle : 0.589 7.405 7436 Z= 0.294 Chirality : 0.038 0.169 867 Planarity : 0.005 0.088 807 Dihedral : 13.034 95.563 1057 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.00 % 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: -0.17 (0.36), residues: 548 helix: 1.00 (0.35), residues: 247 sheet: 0.60 (0.84), residues: 44 loop : -1.39 (0.36), residues: 257 =============================================================================== Job complete usr+sys time: 1259.31 seconds wall clock time: 23 minutes 37.66 seconds (1417.66 seconds total)