Starting phenix.real_space_refine on Thu Sep 26 01:39:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oef_16825/09_2024/8oef_16825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oef_16825/09_2024/8oef_16825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oef_16825/09_2024/8oef_16825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oef_16825/09_2024/8oef_16825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oef_16825/09_2024/8oef_16825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oef_16825/09_2024/8oef_16825.cif" } resolution = 4.0 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= 0.026 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 2315 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: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 3130 2.51 5 N 828 2.21 5 O 848 1.98 5 H 4859 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9687 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9687 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 31, 'TRANS': 580} Chain breaks: 9 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Time building chain proxies: 5.37, per 1000 atoms: 0.55 Number of scatterers: 9687 At special positions: 0 Unit cell: (73.959, 80.607, 114.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 848 8.00 N 828 7.00 C 3130 6.00 H 4859 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 621 " distance=2.03 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: 2.87 Conformation dependent library (CDL) restraints added in 780.4 milliseconds 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 51.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 293 through 307 removed outlier: 3.735A pdb=" N ASP A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 removed outlier: 3.523A pdb=" N ILE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.582A pdb=" N LYS A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.536A pdb=" N LEU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.997A pdb=" N PHE A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 464 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 550 through 564 removed outlier: 4.032A pdb=" N LEU A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.904A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.687A pdb=" N PHE A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1013 removed outlier: 3.692A pdb=" N PHE A1012 " --> pdb=" O CYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.898A pdb=" N ASP A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1090 removed outlier: 3.532A pdb=" N VAL A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A1089 " --> pdb=" O ARG A1085 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1140 removed outlier: 3.614A pdb=" N ILE A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1158 removed outlier: 3.826A pdb=" N LYS A1145 " --> pdb=" O ASP A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1184 Processing helix chain 'A' and resid 1219 through 1224 removed outlier: 3.599A pdb=" N TYR A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1247 removed outlier: 3.520A pdb=" N LEU A1242 " --> pdb=" O TRP A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 removed outlier: 4.391A pdb=" N LYS A1269 " --> pdb=" O THR A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1313 removed outlier: 3.547A pdb=" N ILE A1313 " --> pdb=" O ARG A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1330 Processing helix chain 'A' and resid 1331 through 1336 Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 338 removed outlier: 6.672A pdb=" N VAL A 353 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER A 410 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 355 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 395 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 388 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 399 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP A 384 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 502 removed outlier: 7.102A pdb=" N ILE A 508 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 502 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 535 " --> pdb=" O TRP A 509 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA4, first strand: chain 'A' and resid 1040 through 1045 219 hydrogen bonds defined for protein. 642 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: 3.14 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4845 1.03 - 1.23: 14 1.23 - 1.42: 2021 1.42 - 1.62: 2879 1.62 - 1.81: 30 Bond restraints: 9789 Sorted by residual: bond pdb=" CB ASP A1036 " pdb=" CG ASP A1036 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.03e+00 bond pdb=" CB GLN A 315 " pdb=" CG GLN A 315 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.10e-01 bond pdb=" CB GLN A 402 " pdb=" CG GLN A 402 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.01e-01 bond pdb=" N VAL A 409 " pdb=" CA VAL A 409 " ideal model delta sigma weight residual 1.465 1.475 -0.010 1.38e-02 5.25e+03 4.93e-01 bond pdb=" N ARG A 345 " pdb=" CA ARG A 345 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.54e-01 ... (remaining 9784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.90: 17719 5.90 - 11.80: 0 11.80 - 17.70: 0 17.70 - 23.60: 2 23.60 - 29.50: 4 Bond angle restraints: 17725 Sorted by residual: angle pdb=" CG1 ILE A 618 " pdb=" CD1 ILE A 618 " pdb="HD11 ILE A 618 " ideal model delta sigma weight residual 109.00 79.50 29.50 3.00e+00 1.11e-01 9.67e+01 angle pdb=" CG1 ILE A 618 " pdb=" CD1 ILE A 618 " pdb="HD13 ILE A 618 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.57e+01 angle pdb="HD11 ILE A 618 " pdb=" CD1 ILE A 618 " pdb="HD12 ILE A 618 " ideal model delta sigma weight residual 110.00 81.10 28.90 3.00e+00 1.11e-01 9.28e+01 angle pdb="HD12 ILE A 618 " pdb=" CD1 ILE A 618 " pdb="HD13 ILE A 618 " ideal model delta sigma weight residual 110.00 81.19 28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb="HD11 ILE A 618 " pdb=" CD1 ILE A 618 " pdb="HD13 ILE A 618 " ideal model delta sigma weight residual 110.00 132.66 -22.66 3.00e+00 1.11e-01 5.71e+01 ... (remaining 17720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 4074 16.55 - 33.09: 389 33.09 - 49.63: 102 49.63 - 66.18: 28 66.18 - 82.72: 9 Dihedral angle restraints: 4602 sinusoidal: 2491 harmonic: 2111 Sorted by residual: dihedral pdb=" CA ASP A 597 " pdb=" CB ASP A 597 " pdb=" CG ASP A 597 " pdb=" OD1 ASP A 597 " ideal model delta sinusoidal sigma weight residual -30.00 -86.86 56.86 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG A1132 " pdb=" CD ARG A1132 " pdb=" NE ARG A1132 " pdb=" CZ ARG A1132 " ideal model delta sinusoidal sigma weight residual 90.00 133.77 -43.77 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CB ARG A 534 " pdb=" CG ARG A 534 " pdb=" CD ARG A 534 " pdb=" NE ARG A 534 " ideal model delta sinusoidal sigma weight residual 180.00 126.44 53.56 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 4599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 493 0.025 - 0.050: 170 0.050 - 0.076: 44 0.076 - 0.101: 32 0.101 - 0.126: 28 Chirality restraints: 767 Sorted by residual: chirality pdb=" CA ILE A1189 " pdb=" N ILE A1189 " pdb=" C ILE A1189 " pdb=" CB ILE A1189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 502 " pdb=" N ILE A 502 " pdb=" C ILE A 502 " pdb=" CB ILE A 502 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 764 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1013 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A1014 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1014 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1014 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1017 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ILE A1017 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A1017 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A1018 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1185 " -0.019 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A1186 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A1186 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1186 " -0.015 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 565 2.21 - 2.80: 20212 2.80 - 3.40: 26175 3.40 - 4.00: 32770 4.00 - 4.60: 50327 Nonbonded interactions: 130049 Sorted by model distance: nonbonded pdb=" OE1 GLU A 311 " pdb=" H GLU A 311 " model vdw 1.606 2.450 nonbonded pdb=" H THR A1015 " pdb=" OE1 GLU A1018 " model vdw 1.637 2.450 nonbonded pdb=" O PHE A 561 " pdb=" H PHE A 566 " model vdw 1.689 2.450 nonbonded pdb=" O HIS A1111 " pdb=" H GLY A1115 " model vdw 1.690 2.450 nonbonded pdb=" HH TYR A1171 " pdb=" OD1 ASP A1280 " model vdw 1.706 2.450 ... (remaining 130044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.170 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4623 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 : 0.002 0.027 4930 Z= 0.143 Angle : 0.473 4.775 6673 Z= 0.238 Chirality : 0.037 0.126 767 Planarity : 0.003 0.049 840 Dihedral : 15.212 82.725 1808 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.35), residues: 592 helix: 1.53 (0.32), residues: 253 sheet: -1.02 (0.63), residues: 60 loop : 0.31 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 485 HIS 0.010 0.001 HIS A1090 PHE 0.013 0.001 PHE A 382 TYR 0.014 0.001 TYR A 481 ARG 0.008 0.000 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1149 TYR cc_start: 0.7494 (m-80) cc_final: 0.7122 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.4257 time to fit residues: 35.9585 Evaluate side-chains 66 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4694 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4930 Z= 0.175 Angle : 0.521 5.233 6673 Z= 0.276 Chirality : 0.039 0.155 767 Planarity : 0.004 0.045 840 Dihedral : 3.334 14.477 651 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.57 % Allowed : 10.65 % Favored : 88.78 % 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: 0.96 (0.35), residues: 592 helix: 1.50 (0.31), residues: 263 sheet: -1.00 (0.60), residues: 60 loop : 0.30 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 555 HIS 0.004 0.001 HIS A1090 PHE 0.014 0.001 PHE A 615 TYR 0.014 0.001 TYR A1009 ARG 0.002 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1149 TYR cc_start: 0.7624 (m-80) cc_final: 0.7079 (m-80) REVERT: A 1244 PHE cc_start: 0.4150 (t80) cc_final: 0.3545 (t80) outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.3691 time to fit residues: 35.5685 Evaluate side-chains 69 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1042 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4870 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4930 Z= 0.197 Angle : 0.511 5.007 6673 Z= 0.268 Chirality : 0.039 0.154 767 Planarity : 0.004 0.047 840 Dihedral : 3.501 13.581 651 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.33 % Allowed : 10.27 % Favored : 88.40 % 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: 1.01 (0.35), residues: 592 helix: 1.69 (0.31), residues: 264 sheet: -0.71 (0.65), residues: 55 loop : 0.05 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1238 HIS 0.005 0.001 HIS A 309 PHE 0.011 0.001 PHE A 382 TYR 0.007 0.001 TYR A1171 ARG 0.003 0.000 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1149 TYR cc_start: 0.7600 (m-80) cc_final: 0.7112 (m-80) REVERT: A 1269 LYS cc_start: 0.8740 (tptt) cc_final: 0.8018 (tptt) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.4012 time to fit residues: 38.8797 Evaluate side-chains 77 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1266 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4930 Z= 0.212 Angle : 0.539 9.288 6673 Z= 0.279 Chirality : 0.039 0.146 767 Planarity : 0.004 0.046 840 Dihedral : 3.654 14.367 651 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 9.89 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 592 helix: 1.76 (0.32), residues: 258 sheet: -0.81 (0.67), residues: 55 loop : -0.13 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1238 HIS 0.004 0.001 HIS A 309 PHE 0.013 0.001 PHE A 382 TYR 0.014 0.001 TYR A1009 ARG 0.002 0.000 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1269 LYS cc_start: 0.8739 (tptt) cc_final: 0.8019 (tptt) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.4434 time to fit residues: 42.6551 Evaluate side-chains 77 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 40 optimal weight: 0.0170 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4925 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4930 Z= 0.161 Angle : 0.481 4.591 6673 Z= 0.248 Chirality : 0.039 0.151 767 Planarity : 0.004 0.042 840 Dihedral : 3.548 13.610 651 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.14 % Allowed : 10.84 % Favored : 88.02 % 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: 1.05 (0.35), residues: 592 helix: 1.89 (0.32), residues: 259 sheet: -0.80 (0.67), residues: 55 loop : -0.06 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1238 HIS 0.004 0.001 HIS A1024 PHE 0.021 0.001 PHE A1244 TYR 0.014 0.001 TYR A1009 ARG 0.002 0.000 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1244 PHE cc_start: 0.4450 (t80) cc_final: 0.4220 (t80) REVERT: A 1269 LYS cc_start: 0.8730 (tptt) cc_final: 0.7997 (tptt) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.4052 time to fit residues: 39.8108 Evaluate side-chains 75 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4930 Z= 0.177 Angle : 0.489 4.641 6673 Z= 0.252 Chirality : 0.039 0.147 767 Planarity : 0.004 0.040 840 Dihedral : 3.623 14.956 651 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.52 % Allowed : 11.60 % 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: 0.96 (0.35), residues: 592 helix: 1.90 (0.32), residues: 259 sheet: -1.02 (0.66), residues: 55 loop : -0.15 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1238 HIS 0.004 0.001 HIS A 309 PHE 0.011 0.001 PHE A 382 TYR 0.016 0.001 TYR A1009 ARG 0.005 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 1269 LYS cc_start: 0.8733 (tptt) cc_final: 0.7992 (tptt) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.3753 time to fit residues: 39.5724 Evaluate side-chains 81 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4930 Z= 0.177 Angle : 0.491 4.403 6673 Z= 0.255 Chirality : 0.039 0.144 767 Planarity : 0.004 0.039 840 Dihedral : 3.646 14.152 651 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.90 % Allowed : 11.60 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.35), residues: 592 helix: 1.94 (0.31), residues: 259 sheet: -1.08 (0.67), residues: 55 loop : -0.19 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1238 HIS 0.004 0.001 HIS A 309 PHE 0.022 0.001 PHE A1244 TYR 0.011 0.001 TYR A1009 ARG 0.002 0.000 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 1269 LYS cc_start: 0.8737 (tptt) cc_final: 0.7993 (tptt) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.4014 time to fit residues: 40.8732 Evaluate side-chains 83 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1278 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5214 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4930 Z= 0.279 Angle : 0.583 4.406 6673 Z= 0.314 Chirality : 0.041 0.209 767 Planarity : 0.005 0.041 840 Dihedral : 4.178 16.520 651 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 12.55 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.35), residues: 592 helix: 1.45 (0.31), residues: 259 sheet: -1.30 (0.68), residues: 55 loop : -0.65 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1238 HIS 0.006 0.001 HIS A 309 PHE 0.017 0.002 PHE A1244 TYR 0.023 0.002 TYR A1009 ARG 0.005 0.001 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 454 GLU cc_start: 0.5747 (tt0) cc_final: 0.5446 (tm-30) REVERT: A 1269 LYS cc_start: 0.8728 (tptt) cc_final: 0.8022 (tptt) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.3614 time to fit residues: 39.1112 Evaluate side-chains 84 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1266 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5100 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4930 Z= 0.172 Angle : 0.514 5.140 6673 Z= 0.267 Chirality : 0.039 0.147 767 Planarity : 0.004 0.044 840 Dihedral : 3.898 14.451 651 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.71 % Allowed : 12.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.35), residues: 592 helix: 1.80 (0.31), residues: 259 sheet: -1.14 (0.69), residues: 55 loop : -0.38 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.004 0.001 HIS A1024 PHE 0.009 0.001 PHE A1244 TYR 0.019 0.001 TYR A1009 ARG 0.004 0.000 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 1269 LYS cc_start: 0.8710 (tptt) cc_final: 0.8009 (tptt) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.3156 time to fit residues: 34.5565 Evaluate side-chains 86 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5110 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4930 Z= 0.175 Angle : 0.515 5.039 6673 Z= 0.268 Chirality : 0.040 0.150 767 Planarity : 0.004 0.045 840 Dihedral : 3.861 14.143 651 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.71 % Allowed : 13.69 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 592 helix: 1.91 (0.31), residues: 259 sheet: -1.16 (0.67), residues: 55 loop : -0.39 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1238 HIS 0.004 0.001 HIS A1024 PHE 0.006 0.001 PHE A 440 TYR 0.017 0.001 TYR A1009 ARG 0.003 0.000 ARG A1022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 998 is missing expected H atoms. Skipping. Residue TYR 1137 is missing expected H atoms. Skipping. Residue MET 1151 is missing expected H atoms. Skipping. Residue ILE 1189 is missing expected H atoms. Skipping. Residue MET 1296 is missing expected H atoms. Skipping. Residue THR 1297 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 1269 LYS cc_start: 0.8710 (tptt) cc_final: 0.8015 (tptt) outliers start: 9 outliers final: 9 residues processed: 84 average time/residue: 0.3811 time to fit residues: 40.7253 Evaluate side-chains 87 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1024 HIS ** 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 = 0.4788 r_free = 0.4788 target = 0.200061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.167444 restraints weight = 33710.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.176451 restraints weight = 19700.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.182901 restraints weight = 12490.336| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5135 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4930 Z= 0.153 Angle : 0.495 5.163 6673 Z= 0.257 Chirality : 0.039 0.145 767 Planarity : 0.004 0.044 840 Dihedral : 3.699 13.993 651 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.14 % Allowed : 14.45 % Favored : 84.41 % 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: 1.01 (0.35), residues: 592 helix: 2.14 (0.31), residues: 258 sheet: -1.11 (0.67), residues: 55 loop : -0.32 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1238 HIS 0.003 0.001 HIS A1024 PHE 0.007 0.001 PHE A 389 TYR 0.018 0.001 TYR A1009 ARG 0.004 0.000 ARG A1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2971.84 seconds wall clock time: 62 minutes 20.41 seconds (3740.41 seconds total)