Starting phenix.real_space_refine (version: dev) on Tue Feb 21 09:09:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/02_2023/7zc4_14619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/02_2023/7zc4_14619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/02_2023/7zc4_14619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/02_2023/7zc4_14619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/02_2023/7zc4_14619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/02_2023/7zc4_14619.pdb" } resolution = 3.24 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7224 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7272 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7272 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7254 Classifications: {'peptide': 926} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 62, 'TRANS': 863} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 926, 7254 Classifications: {'peptide': 926} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 62, 'TRANS': 863} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 7404 Time building chain proxies: 7.92, per 1000 atoms: 1.09 Number of scatterers: 7272 At special positions: 0 Unit cell: (79.79, 93.93, 107.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1291 8.00 N 1303 7.00 C 4630 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: 2.94 Conformation dependent library (CDL) restraints added in 2.0 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 69.0% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.565A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.533A pdb=" N ASP A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 463 Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 496 through 520 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.862A pdb=" N CYS A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 568 through 587 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.806A pdb=" N LEU A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 705 " --> pdb=" O GLN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.524A pdb=" N ALA A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 814 through 817 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.122A pdb=" N GLY A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 890 through 907 Processing helix chain 'A' and resid 925 through 935 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 954 through 973 Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 986 through 1000 Processing helix chain 'A' and resid 1008 through 1017 removed outlier: 3.783A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1024 through 1044 Processing helix chain 'A' and resid 1044 through 1063 Processing helix chain 'A' and resid 1111 through 1143 Proline residue: A1120 - end of helix Processing helix chain 'A' and resid 1159 through 1177 Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1197 through 1210 removed outlier: 4.093A pdb=" N GLN A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 3.639A pdb=" N GLN A1221 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA3, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA5, first strand: chain 'A' and resid 919 through 921 removed outlier: 3.952A pdb=" N TYR A1153 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1069 through 1071 465 hydrogen bonds defined for protein. 1359 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: 2.30 Time building geometry restraints manager: 3.25 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: 1472 1.33 - 1.45: 1667 1.45 - 1.57: 4236 1.57 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 7448 Sorted by residual: bond pdb=" CG PHE A 802 " pdb=" CD1 PHE A 802 " ideal model delta sigma weight residual 1.384 1.349 0.035 2.10e-02 2.27e+03 2.73e+00 bond pdb=" CE2 PHE A 802 " pdb=" CZ PHE A 802 " ideal model delta sigma weight residual 1.382 1.333 0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" CA VAL A 603 " pdb=" C VAL A 603 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.10e-02 2.27e+03 1.53e+00 bond pdb=" CA MET A 800 " pdb=" C MET A 800 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.39e-02 5.18e+03 1.46e+00 bond pdb=" CG ASN A 799 " pdb=" OD1 ASN A 799 " ideal model delta sigma weight residual 1.231 1.208 0.023 1.90e-02 2.77e+03 1.44e+00 ... (remaining 7443 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 288 106.21 - 113.16: 4062 113.16 - 120.11: 2524 120.11 - 127.06: 3131 127.06 - 134.01: 124 Bond angle restraints: 10129 Sorted by residual: angle pdb=" N PHE A 802 " pdb=" CA PHE A 802 " pdb=" CB PHE A 802 " ideal model delta sigma weight residual 110.12 116.45 -6.33 1.47e+00 4.63e-01 1.85e+01 angle pdb=" CA PHE A 802 " pdb=" CB PHE A 802 " pdb=" CG PHE A 802 " ideal model delta sigma weight residual 113.80 117.36 -3.56 1.00e+00 1.00e+00 1.27e+01 angle pdb=" C THR A 357 " pdb=" N PHE A 358 " pdb=" CA PHE A 358 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" CA TYR A 999 " pdb=" CB TYR A 999 " pdb=" CG TYR A 999 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.98e+00 angle pdb=" C MET A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.11e+00 ... (remaining 10124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 3963 16.72 - 33.45: 443 33.45 - 50.17: 90 50.17 - 66.90: 23 66.90 - 83.62: 13 Dihedral angle restraints: 4532 sinusoidal: 1811 harmonic: 2721 Sorted by residual: dihedral pdb=" CA ASP A 873 " pdb=" CB ASP A 873 " pdb=" CG ASP A 873 " pdb=" OD1 ASP A 873 " ideal model delta sinusoidal sigma weight residual -30.00 -88.31 58.31 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP A 310 " pdb=" CB ASP A 310 " pdb=" CG ASP A 310 " pdb=" OD1 ASP A 310 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 431 " pdb=" CD ARG A 431 " pdb=" NE ARG A 431 " pdb=" CZ ARG A 431 " ideal model delta sinusoidal sigma weight residual -180.00 -135.03 -44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 4529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 914 0.048 - 0.097: 173 0.097 - 0.145: 43 0.145 - 0.194: 4 0.194 - 0.242: 2 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA HIS A1150 " pdb=" N HIS A1150 " pdb=" C HIS A1150 " pdb=" CB HIS A1150 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA VAL A1149 " pdb=" N VAL A1149 " pdb=" C VAL A1149 " pdb=" CB VAL A1149 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CA PHE A 802 " pdb=" N PHE A 802 " pdb=" C PHE A 802 " pdb=" CB PHE A 802 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1133 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 553 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C TRP A 553 " -0.056 2.00e-02 2.50e+03 pdb=" O TRP A 553 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A 554 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 900 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C GLU A 900 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU A 900 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 901 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 802 " -0.030 2.00e-02 2.50e+03 2.10e-02 7.70e+00 pdb=" CG PHE A 802 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 802 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 802 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 802 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 802 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 802 " -0.012 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 104 2.70 - 3.25: 7490 3.25 - 3.80: 12475 3.80 - 4.35: 15963 4.35 - 4.90: 25657 Nonbonded interactions: 61689 Sorted by model distance: nonbonded pdb=" OE1 GLN A 485 " pdb=" OG1 THR A 640 " model vdw 2.152 2.440 nonbonded pdb=" NH2 ARG A 782 " pdb=" OG SER A 818 " model vdw 2.275 2.520 nonbonded pdb=" NH2 ARG A 411 " pdb=" OE1 GLU A 642 " model vdw 2.278 2.520 nonbonded pdb=" O GLN A 585 " pdb=" NE2 GLN A 588 " model vdw 2.295 2.520 nonbonded pdb=" OD1 ASN A 265 " pdb=" OG SER A 298 " model vdw 2.343 2.440 ... (remaining 61684 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4630 2.51 5 N 1303 2.21 5 O 1291 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 6.420 Check model and map are aligned: 0.110 Process input model: 27.830 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 : 0.003 0.052 7448 Z= 0.218 Angle : 0.662 7.612 10129 Z= 0.362 Chirality : 0.043 0.242 1136 Planarity : 0.005 0.036 1316 Dihedral : 15.191 83.623 2760 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 2.81 (0.28), residues: 917 helix: 2.66 (0.21), residues: 606 sheet: -0.84 (0.98), residues: 32 loop : 0.45 (0.37), residues: 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.854 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2462 time to fit residues: 37.0973 Evaluate side-chains 99 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1165 GLN A1170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7448 Z= 0.251 Angle : 0.619 12.298 10129 Z= 0.310 Chirality : 0.040 0.177 1136 Planarity : 0.005 0.044 1316 Dihedral : 3.730 18.179 1010 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.04 % 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: 2.52 (0.27), residues: 917 helix: 2.34 (0.20), residues: 604 sheet: -0.42 (0.83), residues: 42 loop : 0.58 (0.38), residues: 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.833 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 105 average time/residue: 0.2274 time to fit residues: 31.6489 Evaluate side-chains 95 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1390 time to fit residues: 1.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 588 GLN A 704 ASN ** A 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7448 Z= 0.256 Angle : 0.598 11.839 10129 Z= 0.297 Chirality : 0.040 0.179 1136 Planarity : 0.005 0.058 1316 Dihedral : 3.734 13.548 1010 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.65 % 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: 2.27 (0.27), residues: 917 helix: 2.08 (0.20), residues: 604 sheet: -0.15 (0.80), residues: 42 loop : 0.59 (0.38), residues: 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.2288 time to fit residues: 31.0766 Evaluate side-chains 96 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0696 time to fit residues: 1.4720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 chunk 9 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7448 Z= 0.232 Angle : 0.571 11.405 10129 Z= 0.282 Chirality : 0.038 0.193 1136 Planarity : 0.005 0.045 1316 Dihedral : 3.746 14.982 1010 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.78 % 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: 2.34 (0.27), residues: 917 helix: 2.14 (0.20), residues: 604 sheet: -0.17 (0.79), residues: 42 loop : 0.62 (0.38), residues: 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.771 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.2361 time to fit residues: 30.1132 Evaluate side-chains 92 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1606 time to fit residues: 1.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 79 optimal weight: 0.0020 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.0070 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7448 Z= 0.227 Angle : 0.566 10.156 10129 Z= 0.278 Chirality : 0.038 0.196 1136 Planarity : 0.005 0.047 1316 Dihedral : 3.723 12.987 1010 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.26 % 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: 2.38 (0.27), residues: 917 helix: 2.22 (0.20), residues: 605 sheet: -0.24 (0.79), residues: 42 loop : 0.52 (0.37), residues: 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.798 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.2296 time to fit residues: 28.6080 Evaluate side-chains 91 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0738 time to fit residues: 1.3947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 7448 Z= 0.296 Angle : 0.609 10.698 10129 Z= 0.299 Chirality : 0.040 0.217 1136 Planarity : 0.005 0.075 1316 Dihedral : 3.929 14.706 1010 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.26 % 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: 2.14 (0.27), residues: 917 helix: 2.05 (0.20), residues: 603 sheet: -0.24 (0.81), residues: 42 loop : 0.36 (0.36), residues: 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.769 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 96 average time/residue: 0.2338 time to fit residues: 29.4829 Evaluate side-chains 93 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0809 time to fit residues: 1.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 7448 Z= 0.325 Angle : 0.630 11.611 10129 Z= 0.310 Chirality : 0.041 0.229 1136 Planarity : 0.005 0.047 1316 Dihedral : 4.005 15.092 1010 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.26 % 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: 1.96 (0.27), residues: 917 helix: 1.86 (0.20), residues: 602 sheet: -0.01 (1.01), residues: 32 loop : 0.36 (0.35), residues: 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.738 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.2326 time to fit residues: 29.3972 Evaluate side-chains 92 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0869 time to fit residues: 1.3024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.0020 chunk 84 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7448 Z= 0.259 Angle : 0.593 12.449 10129 Z= 0.290 Chirality : 0.039 0.261 1136 Planarity : 0.005 0.050 1316 Dihedral : 3.901 14.212 1010 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.26 % 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: 2.04 (0.27), residues: 917 helix: 1.94 (0.20), residues: 603 sheet: 0.00 (1.03), residues: 32 loop : 0.34 (0.35), residues: 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.869 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 98 average time/residue: 0.2431 time to fit residues: 31.6909 Evaluate side-chains 96 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0719 time to fit residues: 1.2637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7448 Z= 0.260 Angle : 0.615 12.811 10129 Z= 0.299 Chirality : 0.039 0.239 1136 Planarity : 0.005 0.051 1316 Dihedral : 3.917 14.196 1010 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.52 % 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: 2.06 (0.27), residues: 917 helix: 1.95 (0.21), residues: 603 sheet: -0.01 (1.02), residues: 32 loop : 0.37 (0.36), residues: 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.878 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.2285 time to fit residues: 29.1622 Evaluate side-chains 94 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0959 time to fit residues: 1.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0370 chunk 60 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 7 optimal weight: 0.0570 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7448 Z= 0.175 Angle : 0.582 13.454 10129 Z= 0.280 Chirality : 0.037 0.285 1136 Planarity : 0.005 0.051 1316 Dihedral : 3.804 20.982 1010 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.26 % 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: 2.38 (0.27), residues: 917 helix: 2.18 (0.21), residues: 603 sheet: 0.13 (1.02), residues: 32 loop : 0.53 (0.36), residues: 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.784 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.2460 time to fit residues: 29.8913 Evaluate side-chains 88 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 73 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.1072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.205462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.179459 restraints weight = 20507.807| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 3.51 r_work: 0.4109 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4553 r_free = 0.4553 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4553 r_free = 0.4553 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 7448 Z= 0.152 Angle : 0.565 13.586 10129 Z= 0.271 Chirality : 0.036 0.231 1136 Planarity : 0.005 0.061 1316 Dihedral : 3.646 20.051 1010 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.26 % 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: 2.62 (0.27), residues: 917 helix: 2.32 (0.21), residues: 605 sheet: 0.09 (1.03), residues: 32 loop : 0.76 (0.37), residues: 280 =============================================================================== Job complete usr+sys time: 1811.97 seconds wall clock time: 33 minutes 16.58 seconds (1996.58 seconds total)