Starting phenix.real_space_refine on Thu Sep 26 12:43:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/09_2024/7zc4_14619.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/09_2024/7zc4_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_14619/09_2024/7zc4_14619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/09_2024/7zc4_14619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/09_2024/7zc4_14619.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc4_14619/09_2024/7zc4_14619.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.09, per 1000 atoms: 1.11 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 - 3.00 Amino acid : True - 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: 2.19 Conformation dependent library (CDL) restraints added in 1.9 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: 0.75 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: 2.32 Time building geometry restraints manager: 2.47 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: 0.00 - 1.52: 9732 1.52 - 3.04: 324 3.04 - 4.57: 54 4.57 - 6.09: 15 6.09 - 7.61: 4 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 3.040 nonbonded pdb=" NH2 ARG A 782 " pdb=" OG SER A 818 " model vdw 2.275 3.120 nonbonded pdb=" NH2 ARG A 411 " pdb=" OE1 GLU A 642 " model vdw 2.278 3.120 nonbonded pdb=" O GLN A 585 " pdb=" NE2 GLN A 588 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASN A 265 " pdb=" OG SER A 298 " model vdw 2.343 3.040 ... (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 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: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 25.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 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 % Allowed : 0.26 % Favored : 99.74 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 553 HIS 0.011 0.001 HIS A1150 PHE 0.045 0.002 PHE A 802 TYR 0.025 0.002 TYR A 461 ARG 0.006 0.001 ARG A 477 *********************** 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 : 0.783 Fit side-chains REVERT: A 269 LEU cc_start: 0.7496 (mm) cc_final: 0.7283 (mm) REVERT: A 533 TYR cc_start: 0.5654 (t80) cc_final: 0.5216 (t80) REVERT: A 778 GLU cc_start: 0.6536 (tm-30) cc_final: 0.6189 (tp30) REVERT: A 987 ARG cc_start: 0.6277 (tmt170) cc_final: 0.5949 (tmt170) REVERT: A 1154 TRP cc_start: 0.6101 (m-10) cc_final: 0.5034 (m-10) REVERT: A 1177 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6457 (mp0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2440 time to fit residues: 36.8724 Evaluate side-chains 101 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 0.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 A 659 HIS A 893 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7448 Z= 0.293 Angle : 0.647 13.271 10129 Z= 0.325 Chirality : 0.042 0.172 1136 Planarity : 0.005 0.051 1316 Dihedral : 3.852 17.014 1010 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.78 % Allowed : 7.27 % Favored : 91.95 % 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: 2.33 (0.27), residues: 917 helix: 2.18 (0.20), residues: 604 sheet: -0.59 (0.81), residues: 42 loop : 0.55 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1154 HIS 0.007 0.001 HIS A 512 PHE 0.024 0.002 PHE A 802 TYR 0.018 0.002 TYR A 299 ARG 0.006 0.001 ARG A 516 *********************** 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: 6 poor density : 104 time to evaluate : 0.773 Fit side-chains REVERT: A 269 LEU cc_start: 0.7744 (mm) cc_final: 0.7501 (mm) REVERT: A 403 GLN cc_start: 0.6054 (tp40) cc_final: 0.5690 (tp40) REVERT: A 503 GLU cc_start: 0.6161 (tp30) cc_final: 0.5811 (tp30) REVERT: A 515 GLN cc_start: 0.5686 (OUTLIER) cc_final: 0.5432 (mp10) REVERT: A 669 LYS cc_start: 0.6590 (mmtt) cc_final: 0.6335 (mmpt) REVERT: A 704 ASN cc_start: 0.5652 (m-40) cc_final: 0.5276 (m110) REVERT: A 852 LYS cc_start: 0.7233 (mmmt) cc_final: 0.6897 (mmmm) REVERT: A 859 LYS cc_start: 0.6853 (mmtp) cc_final: 0.6536 (mptt) REVERT: A 993 THR cc_start: 0.6115 (t) cc_final: 0.5838 (t) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2444 time to fit residues: 33.3005 Evaluate side-chains 104 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 772 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 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: 0.5759 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7448 Z= 0.288 Angle : 0.611 11.768 10129 Z= 0.305 Chirality : 0.041 0.212 1136 Planarity : 0.005 0.074 1316 Dihedral : 3.840 13.665 1010 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.43 % Allowed : 8.18 % Favored : 90.39 % 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: 2.13 (0.27), residues: 917 helix: 1.98 (0.20), residues: 604 sheet: -0.44 (0.80), residues: 42 loop : 0.57 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1154 HIS 0.005 0.001 HIS A1125 PHE 0.020 0.002 PHE A 802 TYR 0.016 0.002 TYR A 299 ARG 0.011 0.001 ARG A 516 *********************** 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 108 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7828 (mm) cc_final: 0.7597 (mm) REVERT: A 403 GLN cc_start: 0.6140 (tp40) cc_final: 0.4906 (tp40) REVERT: A 503 GLU cc_start: 0.6208 (tp30) cc_final: 0.5848 (tp30) REVERT: A 690 THR cc_start: 0.5130 (OUTLIER) cc_final: 0.4792 (p) REVERT: A 854 ARG cc_start: 0.6581 (ptp-110) cc_final: 0.6238 (ttm-80) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.2545 time to fit residues: 33.2364 Evaluate side-chains 101 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.2476 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= 0.218 Angle : 0.568 10.250 10129 Z= 0.281 Chirality : 0.038 0.180 1136 Planarity : 0.005 0.044 1316 Dihedral : 3.763 13.947 1010 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.04 % Allowed : 9.87 % Favored : 89.09 % 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: 2.26 (0.27), residues: 917 helix: 2.09 (0.20), residues: 605 sheet: -0.33 (0.77), residues: 42 loop : 0.57 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1154 HIS 0.006 0.001 HIS A 512 PHE 0.025 0.002 PHE A1186 TYR 0.014 0.001 TYR A 999 ARG 0.008 0.000 ARG A 516 *********************** 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 105 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7834 (mm) cc_final: 0.7622 (mm) REVERT: A 403 GLN cc_start: 0.6112 (tp40) cc_final: 0.4808 (tp40) REVERT: A 503 GLU cc_start: 0.6177 (tp30) cc_final: 0.5832 (tp30) REVERT: A 522 GLN cc_start: 0.6896 (tp40) cc_final: 0.6496 (tp40) REVERT: A 729 LEU cc_start: 0.6724 (mt) cc_final: 0.6320 (mt) outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 0.2697 time to fit residues: 35.1274 Evaluate side-chains 98 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.2759 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= 0.264 Angle : 0.582 12.255 10129 Z= 0.287 Chirality : 0.039 0.171 1136 Planarity : 0.005 0.044 1316 Dihedral : 3.790 14.801 1010 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.30 % Allowed : 10.78 % Favored : 87.92 % 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: 2.19 (0.27), residues: 917 helix: 2.02 (0.20), residues: 605 sheet: -0.25 (0.94), residues: 32 loop : 0.56 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1154 HIS 0.006 0.001 HIS A1125 PHE 0.018 0.002 PHE A 802 TYR 0.012 0.001 TYR A 931 ARG 0.006 0.000 ARG A 450 *********************** 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 106 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7839 (mm) cc_final: 0.7627 (mm) REVERT: A 503 GLU cc_start: 0.6221 (tp30) cc_final: 0.5841 (tp30) REVERT: A 515 GLN cc_start: 0.6148 (mm-40) cc_final: 0.5740 (mp10) REVERT: A 831 ARG cc_start: 0.5997 (tpt170) cc_final: 0.5671 (tpt170) REVERT: A 899 MET cc_start: 0.4200 (mtt) cc_final: 0.3824 (mtt) REVERT: A 993 THR cc_start: 0.6180 (t) cc_final: 0.5945 (t) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.2396 time to fit residues: 30.9716 Evaluate side-chains 99 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 953 GLN Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 659 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5766 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7448 Z= 0.241 Angle : 0.570 11.182 10129 Z= 0.281 Chirality : 0.038 0.164 1136 Planarity : 0.005 0.044 1316 Dihedral : 3.790 14.905 1010 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.17 % Allowed : 10.78 % Favored : 88.05 % 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: 2.24 (0.27), residues: 917 helix: 2.05 (0.20), residues: 605 sheet: -0.22 (0.96), residues: 32 loop : 0.57 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1154 HIS 0.005 0.001 HIS A1125 PHE 0.018 0.002 PHE A1217 TYR 0.014 0.001 TYR A1227 ARG 0.005 0.000 ARG A 450 *********************** 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 99 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7829 (mm) cc_final: 0.7620 (mm) REVERT: A 503 GLU cc_start: 0.6195 (tp30) cc_final: 0.5844 (tp30) REVERT: A 522 GLN cc_start: 0.7031 (tp40) cc_final: 0.6601 (tp40) REVERT: A 831 ARG cc_start: 0.6014 (tpt170) cc_final: 0.5666 (tpt170) REVERT: A 899 MET cc_start: 0.4165 (mtt) cc_final: 0.3811 (mtt) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.2379 time to fit residues: 29.2449 Evaluate side-chains 94 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 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: 0.5803 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7448 Z= 0.295 Angle : 0.606 12.083 10129 Z= 0.299 Chirality : 0.040 0.222 1136 Planarity : 0.005 0.045 1316 Dihedral : 3.911 15.299 1010 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.43 % Allowed : 10.91 % Favored : 87.66 % 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: 2.05 (0.27), residues: 917 helix: 1.92 (0.20), residues: 604 sheet: -0.04 (0.99), residues: 32 loop : 0.42 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1154 HIS 0.006 0.001 HIS A1125 PHE 0.020 0.002 PHE A 802 TYR 0.015 0.002 TYR A1227 ARG 0.004 0.000 ARG A 450 *********************** 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 106 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7849 (mm) cc_final: 0.7634 (mm) REVERT: A 286 MET cc_start: 0.5388 (ttp) cc_final: 0.5163 (ttp) REVERT: A 503 GLU cc_start: 0.6144 (tp30) cc_final: 0.5799 (tp30) REVERT: A 831 ARG cc_start: 0.6081 (tpt170) cc_final: 0.5703 (tpt170) REVERT: A 899 MET cc_start: 0.4149 (mtt) cc_final: 0.3824 (mtt) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.2224 time to fit residues: 30.3734 Evaluate side-chains 100 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 953 GLN Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** A1122 ASN A1209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.3243 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= 0.262 Angle : 0.592 12.086 10129 Z= 0.290 Chirality : 0.039 0.212 1136 Planarity : 0.005 0.047 1316 Dihedral : 3.876 15.753 1010 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.30 % Allowed : 11.82 % Favored : 86.88 % 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: 2.13 (0.27), residues: 917 helix: 1.99 (0.20), residues: 604 sheet: 0.05 (0.98), residues: 32 loop : 0.43 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1154 HIS 0.006 0.001 HIS A1125 PHE 0.018 0.002 PHE A 802 TYR 0.015 0.002 TYR A1227 ARG 0.004 0.000 ARG A 516 *********************** 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 98 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 THR cc_start: 0.7932 (t) cc_final: 0.7566 (p) REVERT: A 269 LEU cc_start: 0.7815 (mm) cc_final: 0.7603 (mm) REVERT: A 503 GLU cc_start: 0.6144 (tp30) cc_final: 0.5803 (tp30) REVERT: A 515 GLN cc_start: 0.5976 (mm-40) cc_final: 0.5709 (mm110) REVERT: A 831 ARG cc_start: 0.6097 (tpt170) cc_final: 0.5693 (tpt170) REVERT: A 899 MET cc_start: 0.4160 (mtt) cc_final: 0.3855 (mtt) outliers start: 9 outliers final: 8 residues processed: 96 average time/residue: 0.2206 time to fit residues: 28.2830 Evaluate side-chains 95 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 953 GLN Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.0270 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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: 0.5765 moved from start: 0.3335 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= 0.216 Angle : 0.577 11.698 10129 Z= 0.282 Chirality : 0.037 0.164 1136 Planarity : 0.005 0.047 1316 Dihedral : 3.769 15.720 1010 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.91 % Allowed : 12.99 % Favored : 86.10 % 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: 2.32 (0.28), residues: 917 helix: 2.12 (0.21), residues: 605 sheet: -0.02 (0.98), residues: 32 loop : 0.54 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1154 HIS 0.005 0.001 HIS A1125 PHE 0.016 0.002 PHE A 802 TYR 0.011 0.001 TYR A1227 ARG 0.004 0.000 ARG A 450 *********************** 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 94 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7815 (mm) cc_final: 0.7603 (mm) REVERT: A 282 TYR cc_start: 0.6577 (t80) cc_final: 0.6317 (t80) REVERT: A 503 GLU cc_start: 0.6145 (tp30) cc_final: 0.5802 (tp30) REVERT: A 515 GLN cc_start: 0.5959 (mm-40) cc_final: 0.5708 (mm110) REVERT: A 522 GLN cc_start: 0.7100 (tp40) cc_final: 0.6610 (tp40) REVERT: A 831 ARG cc_start: 0.6070 (tpt170) cc_final: 0.5660 (tpt170) REVERT: A 899 MET cc_start: 0.4217 (mtt) cc_final: 0.3901 (mtt) outliers start: 6 outliers final: 6 residues processed: 92 average time/residue: 0.2167 time to fit residues: 27.0184 Evaluate side-chains 95 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 953 GLN Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.5803 moved from start: 0.3428 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= 0.288 Angle : 0.616 11.095 10129 Z= 0.302 Chirality : 0.039 0.226 1136 Planarity : 0.005 0.050 1316 Dihedral : 3.913 15.182 1010 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.17 % Allowed : 12.99 % Favored : 85.84 % 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: 1.98 (0.21), residues: 604 sheet: 0.02 (0.98), residues: 32 loop : 0.50 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1154 HIS 0.008 0.001 HIS A1125 PHE 0.019 0.002 PHE A 802 TYR 0.016 0.002 TYR A 999 ARG 0.004 0.000 ARG A 450 ********************** 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 96 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7827 (mm) cc_final: 0.7618 (mm) REVERT: A 282 TYR cc_start: 0.6595 (t80) cc_final: 0.6293 (t80) REVERT: A 522 GLN cc_start: 0.7192 (tp40) cc_final: 0.6679 (tp40) REVERT: A 805 ARG cc_start: 0.5298 (OUTLIER) cc_final: 0.5049 (mmt90) REVERT: A 831 ARG cc_start: 0.6121 (tpt170) cc_final: 0.5707 (tpt170) REVERT: A 899 MET cc_start: 0.4156 (mtt) cc_final: 0.3850 (mtt) outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 0.2285 time to fit residues: 28.1740 Evaluate side-chains 96 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 953 GLN Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1148 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 515 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.201032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174253 restraints weight = 20358.989| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.50 r_work: 0.4070 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 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= 0.220 Angle : 0.578 11.508 10129 Z= 0.282 Chirality : 0.037 0.174 1136 Planarity : 0.005 0.052 1316 Dihedral : 3.816 15.067 1010 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.17 % Allowed : 12.99 % Favored : 85.84 % 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: 2.28 (0.28), residues: 917 helix: 2.08 (0.21), residues: 605 sheet: -0.08 (0.97), residues: 32 loop : 0.57 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1154 HIS 0.005 0.001 HIS A1125 PHE 0.016 0.002 PHE A 802 TYR 0.013 0.001 TYR A 999 ARG 0.004 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.07 seconds wall clock time: 35 minutes 0.18 seconds (2100.18 seconds total)