Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 18:41:19 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/12_2021/6xmu_22264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/12_2021/6xmu_22264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/12_2021/6xmu_22264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/12_2021/6xmu_22264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/12_2021/6xmu_22264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/12_2021/6xmu_22264_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8306 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 49, 'TRANS': 1040} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.20, per 1000 atoms: 0.62 Number of scatterers: 8411 At special positions: 0 Unit cell: (91.63, 88.06, 145.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 38 16.00 Mg 1 11.99 F 3 9.00 O 1548 8.00 N 1398 7.00 C 5422 6.00 Be 1 4.00 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 Amimo 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 8 sheets defined 42.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 27 through 43 Proline residue: A 31 - end of helix Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.215A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 219 through 246 Processing helix chain 'A' and resid 333 through 336 removed outlier: 4.322A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 397 through 424 Processing helix chain 'A' and resid 428 through 441 Processing helix chain 'A' and resid 447 through 465 removed outlier: 3.985A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 476 through 479 removed outlier: 3.531A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.790A pdb=" N GLY A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.551A pdb=" N SER A 689 " --> pdb=" O MET A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 767 through 772 Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'A' and resid 794 through 806 removed outlier: 4.453A pdb=" N GLU A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 971 through 1011 removed outlier: 3.901A pdb=" N ARG A 982 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A1008 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A1010 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.889A pdb=" N LEU A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1083 Processing helix chain 'A' and resid 1100 through 1118 removed outlier: 4.074A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'A' and resid 1169 through 1196 Processing helix chain 'B' and resid 2 through 19 Processing sheet with id= A, first strand: chain 'A' and resid 111 through 114 Processing sheet with id= B, first strand: chain 'A' and resid 256 through 260 Processing sheet with id= C, first strand: chain 'A' and resid 277 through 280 removed outlier: 7.092A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 467 through 469 Processing sheet with id= E, first strand: chain 'A' and resid 664 through 667 removed outlier: 7.252A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 742 through 744 removed outlier: 3.732A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP A 762 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU A 721 " --> pdb=" O ASP A 762 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 764 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ARG A 723 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP A 787 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 765 " --> pdb=" O TRP A 787 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A 789 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.829A pdb=" N GLN A 347 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN A 303 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 345 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.852A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2701 1.34 - 1.46: 1481 1.46 - 1.57: 4335 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8580 Sorted by residual: bond pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" F3 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" F1 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.19e-02 7.06e+03 4.64e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.23e-02 6.61e+03 3.56e+00 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.91: 203 105.91 - 112.95: 4735 112.95 - 119.99: 2808 119.99 - 127.03: 3814 127.03 - 134.07: 87 Bond angle restraints: 11647 Sorted by residual: angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 110.53 117.10 -6.57 9.40e-01 1.13e+00 4.88e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 118.85 126.10 -7.25 1.09e+00 8.42e-01 4.43e+01 angle pdb=" N PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta sigma weight residual 103.33 109.78 -6.45 1.10e+00 8.26e-01 3.44e+01 angle pdb=" C LYS A 26 " pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 119.05 125.22 -6.17 1.11e+00 8.12e-01 3.09e+01 angle pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.22 12.74 3.00e+00 1.11e-01 1.80e+01 ... (remaining 11642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4791 17.94 - 35.88: 302 35.88 - 53.81: 38 53.81 - 71.75: 6 71.75 - 89.69: 4 Dihedral angle restraints: 5141 sinusoidal: 1922 harmonic: 3219 Sorted by residual: dihedral pdb=" CA TYR A 761 " pdb=" C TYR A 761 " pdb=" N ASP A 762 " pdb=" CA ASP A 762 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR A1121 " pdb=" C TYR A1121 " pdb=" N GLN A1122 " pdb=" CA GLN A1122 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta harmonic sigma weight residual 115.10 123.27 -8.17 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 5138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1140 0.052 - 0.105: 194 0.105 - 0.157: 32 0.157 - 0.210: 2 0.210 - 0.262: 3 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU A 30 " pdb=" CB LEU A 30 " pdb=" CD1 LEU A 30 " pdb=" CD2 LEU A 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1368 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C VAL A 29 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 31 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1006 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.81e+00 pdb=" C LEU A1006 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A1006 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A1007 " 0.010 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 41 2.54 - 3.13: 6578 3.13 - 3.72: 12161 3.72 - 4.31: 16144 4.31 - 4.90: 28136 Nonbonded interactions: 63060 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.956 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.959 2.390 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1302 " model vdw 2.194 2.170 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 516 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A1099 " pdb=" OD1 ASN A1102 " model vdw 2.241 2.440 ... (remaining 63055 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 5422 2.51 5 N 1398 2.21 5 O 1548 1.98 5 F 3 1.80 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 individual isotropic Write .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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.190 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 25.880 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.004 0.084 8580 Z= 0.248 Angle : 0.585 12.740 11647 Z= 0.329 Chirality : 0.042 0.262 1371 Planarity : 0.004 0.042 1478 Dihedral : 11.801 89.690 3053 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.43 (0.22), residues: 1080 helix: 0.00 (0.22), residues: 478 sheet: -2.86 (0.40), residues: 120 loop : -3.02 (0.21), residues: 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.997 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1939 time to fit residues: 15.4472 Evaluate side-chains 37 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.0040 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 107 ASN A 196 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS A 990 GLN A1050 GLN A1122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8580 Z= 0.154 Angle : 0.496 7.769 11647 Z= 0.254 Chirality : 0.039 0.171 1371 Planarity : 0.004 0.033 1478 Dihedral : 3.785 19.894 1167 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.24), residues: 1080 helix: 0.76 (0.24), residues: 483 sheet: -2.80 (0.36), residues: 142 loop : -2.50 (0.23), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.954 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.1660 time to fit residues: 11.0778 Evaluate side-chains 38 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0814 time to fit residues: 1.7413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8580 Z= 0.220 Angle : 0.518 12.986 11647 Z= 0.255 Chirality : 0.040 0.179 1371 Planarity : 0.004 0.035 1478 Dihedral : 3.798 19.618 1167 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.25), residues: 1080 helix: 1.02 (0.25), residues: 482 sheet: -2.68 (0.36), residues: 148 loop : -2.25 (0.24), residues: 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 1.300 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.1704 time to fit residues: 11.9948 Evaluate side-chains 40 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0845 time to fit residues: 1.9035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8580 Z= 0.229 Angle : 0.498 11.105 11647 Z= 0.250 Chirality : 0.040 0.176 1371 Planarity : 0.004 0.035 1478 Dihedral : 3.803 19.769 1167 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.25), residues: 1080 helix: 1.26 (0.25), residues: 475 sheet: -2.37 (0.37), residues: 147 loop : -1.97 (0.25), residues: 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 1.054 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 0.1684 time to fit residues: 12.4259 Evaluate side-chains 40 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0940 time to fit residues: 1.9446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8580 Z= 0.252 Angle : 0.515 10.329 11647 Z= 0.257 Chirality : 0.040 0.190 1371 Planarity : 0.004 0.036 1478 Dihedral : 3.839 19.965 1167 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.25), residues: 1080 helix: 1.38 (0.25), residues: 474 sheet: -2.21 (0.38), residues: 147 loop : -1.85 (0.25), residues: 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 1.036 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 0.1565 time to fit residues: 11.8577 Evaluate side-chains 41 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0870 time to fit residues: 1.7981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 0.0970 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8580 Z= 0.150 Angle : 0.479 11.527 11647 Z= 0.240 Chirality : 0.039 0.196 1371 Planarity : 0.003 0.033 1478 Dihedral : 3.661 19.827 1167 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1080 helix: 1.51 (0.25), residues: 474 sheet: -1.80 (0.40), residues: 140 loop : -1.75 (0.25), residues: 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 1.079 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 46 average time/residue: 0.1640 time to fit residues: 12.5103 Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0810 time to fit residues: 1.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8580 Z= 0.141 Angle : 0.504 11.783 11647 Z= 0.244 Chirality : 0.039 0.211 1371 Planarity : 0.003 0.033 1478 Dihedral : 3.595 19.353 1167 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.25), residues: 1080 helix: 1.61 (0.25), residues: 473 sheet: -1.59 (0.40), residues: 140 loop : -1.64 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 1.094 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 45 average time/residue: 0.1670 time to fit residues: 12.5675 Evaluate side-chains 41 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0810 time to fit residues: 1.8784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8580 Z= 0.249 Angle : 0.530 12.235 11647 Z= 0.264 Chirality : 0.040 0.201 1371 Planarity : 0.005 0.109 1478 Dihedral : 3.752 19.947 1167 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.25), residues: 1080 helix: 1.70 (0.25), residues: 473 sheet: -1.56 (0.41), residues: 140 loop : -1.61 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 1.108 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.1681 time to fit residues: 12.1252 Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0806 time to fit residues: 1.7402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8580 Z= 0.163 Angle : 0.516 11.501 11647 Z= 0.252 Chirality : 0.041 0.301 1371 Planarity : 0.004 0.097 1478 Dihedral : 3.652 19.980 1167 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.25), residues: 1080 helix: 1.76 (0.25), residues: 470 sheet: -1.41 (0.41), residues: 140 loop : -1.53 (0.25), residues: 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 1.022 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1661 time to fit residues: 11.4239 Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0811 time to fit residues: 1.6579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8580 Z= 0.166 Angle : 0.505 11.285 11647 Z= 0.249 Chirality : 0.040 0.249 1371 Planarity : 0.004 0.094 1478 Dihedral : 3.591 19.788 1167 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.26), residues: 1080 helix: 1.85 (0.25), residues: 472 sheet: -1.24 (0.42), residues: 140 loop : -1.45 (0.26), residues: 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1925 time to fit residues: 12.2222 Evaluate side-chains 37 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.077386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056553 restraints weight = 29226.244| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.41 r_work: 0.3099 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work: 0.3076 rms_B_bonded: 3.16 restraints_weight: 0.1250 r_work: 0.3064 rms_B_bonded: 3.23 restraints_weight: 0.0625 r_work: 0.3052 rms_B_bonded: 3.33 restraints_weight: 0.0312 r_work: 0.3040 rms_B_bonded: 3.46 restraints_weight: 0.0156 r_work: 0.3026 rms_B_bonded: 3.61 restraints_weight: 0.0078 r_work: 0.3012 rms_B_bonded: 3.80 restraints_weight: 0.0039 r_work: 0.2997 rms_B_bonded: 4.03 restraints_weight: 0.0020 r_work: 0.2982 rms_B_bonded: 4.28 restraints_weight: 0.0010 r_work: 0.2965 rms_B_bonded: 4.58 restraints_weight: 0.0005 r_work: 0.2947 rms_B_bonded: 4.92 restraints_weight: 0.0002 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 8580 Z= 0.167 Angle : 0.511 11.694 11647 Z= 0.250 Chirality : 0.040 0.224 1371 Planarity : 0.004 0.114 1478 Dihedral : 3.579 19.684 1167 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1080 helix: 1.87 (0.25), residues: 472 sheet: -1.27 (0.40), residues: 151 loop : -1.44 (0.26), residues: 457 =============================================================================== Job complete usr+sys time: 1489.83 seconds wall clock time: 28 minutes 17.16 seconds (1697.16 seconds total)