Starting phenix.real_space_refine on Fri Mar 15 07:23:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/03_2024/7ppo_13583_updated.pdb" } resolution = 2.91 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 6974 2.51 5 N 1875 2.21 5 O 2103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "A TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 542": "OD1" <-> "OD2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10990 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4003 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, '86N:plan-4': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 6099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6099 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 717} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 886 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 137 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.01, per 1000 atoms: 0.55 Number of scatterers: 10990 At special positions: 0 Unit cell: (139.104, 104.832, 92.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 35 16.00 P 1 15.00 Mg 1 11.99 O 2103 8.00 N 1875 7.00 C 6974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.0 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 7 sheets defined 48.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 279 through 301 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 344 through 364 Processing helix chain 'A' and resid 367 through 370 No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.675A pdb=" N HIS A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 removed outlier: 3.773A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 451 removed outlier: 3.606A pdb=" N ALA A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.760A pdb=" N LYS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.073A pdb=" N ASN A 527 " --> pdb=" O PRO A 523 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 528' Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.543A pdb=" N TRP A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN A 550 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 564 through 586 Proline residue: A 582 - end of helix Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.713A pdb=" N GLN A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 807 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'C' and resid 136 through 157 removed outlier: 4.067A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 Processing helix chain 'C' and resid 165 through 181 Processing helix chain 'C' and resid 185 through 205 Proline residue: C 197 - end of helix Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.507A pdb=" N GLU C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 237 through 245 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 271 through 282 removed outlier: 4.119A pdb=" N TYR C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 4.072A pdb=" N THR C 306 " --> pdb=" O HIS C 302 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 390 Processing helix chain 'C' and resid 392 through 395 No H-bonds generated for 'chain 'C' and resid 392 through 395' Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 425 through 431 Processing helix chain 'C' and resid 447 through 450 Processing helix chain 'C' and resid 460 through 480 Processing helix chain 'C' and resid 494 through 499 removed outlier: 5.732A pdb=" N ASP C 498 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 551 No H-bonds generated for 'chain 'C' and resid 549 through 551' Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 564 through 568 Processing helix chain 'C' and resid 588 through 591 Processing helix chain 'C' and resid 594 through 621 Processing helix chain 'C' and resid 628 through 654 Processing helix chain 'C' and resid 658 through 668 removed outlier: 3.766A pdb=" N ARG C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 681 Processing helix chain 'C' and resid 684 through 687 Processing helix chain 'C' and resid 691 through 702 removed outlier: 3.667A pdb=" N SER C 700 " --> pdb=" O MET C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 770 removed outlier: 3.585A pdb=" N GLN C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 794 Processing helix chain 'C' and resid 800 through 816 Processing helix chain 'C' and resid 826 through 847 removed outlier: 3.843A pdb=" N PHE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.620A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.804A pdb=" N MET B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 83 through 93 removed outlier: 4.010A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 removed outlier: 3.927A pdb=" N THR B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 139 through 143 Processing sheet with id= A, first strand: chain 'A' and resid 265 through 267 Processing sheet with id= B, first strand: chain 'A' and resid 763 through 768 removed outlier: 6.386A pdb=" N TYR A 891 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 839 " --> pdb=" O TYR A 891 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 893 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU A 841 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE A 895 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 818 through 822 Processing sheet with id= D, first strand: chain 'C' and resid 105 through 109 Processing sheet with id= E, first strand: chain 'C' and resid 121 through 124 Processing sheet with id= F, first strand: chain 'C' and resid 403 through 411 removed outlier: 6.693A pdb=" N VAL C 442 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 407 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 440 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C 409 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 438 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 348 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER C 357 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 346 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 27 through 29 463 hydrogen bonds defined for protein. 1350 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: 3.57 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3615 1.34 - 1.47: 2743 1.47 - 1.60: 4794 1.60 - 1.73: 1 1.73 - 1.87: 68 Bond restraints: 11221 Sorted by residual: bond pdb=" O3P 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.510 1.765 -0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" OE1 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.649 1.866 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O2P 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.510 1.692 -0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" CD 86N A 860 " pdb=" OE1 86N A 860 " ideal model delta sigma weight residual 1.400 1.244 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" O5' 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.649 1.765 -0.116 2.00e-02 2.50e+03 3.37e+01 ... (remaining 11216 not shown) Histogram of bond angle deviations from ideal: 95.13 - 107.45: 385 107.45 - 119.78: 9410 119.78 - 132.10: 5363 132.10 - 144.42: 14 144.42 - 156.74: 1 Bond angle restraints: 15173 Sorted by residual: angle pdb=" CA 86N A 860 " pdb=" CB 86N A 860 " pdb=" CG 86N A 860 " ideal model delta sigma weight residual 109.47 156.74 -47.27 3.00e+00 1.11e-01 2.48e+02 angle pdb=" CB 86N A 860 " pdb=" CG 86N A 860 " pdb=" CD 86N A 860 " ideal model delta sigma weight residual 109.47 132.18 -22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" OE1 86N A 860 " pdb=" P 86N A 860 " pdb=" O5' 86N A 860 " ideal model delta sigma weight residual 109.47 127.40 -17.93 3.00e+00 1.11e-01 3.57e+01 angle pdb=" OE1 86N A 860 " pdb=" P 86N A 860 " pdb=" O2P 86N A 860 " ideal model delta sigma weight residual 109.47 95.13 14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" OE1 86N A 860 " pdb=" CD 86N A 860 " pdb=" OE2 86N A 860 " ideal model delta sigma weight residual 120.00 130.89 -10.89 3.00e+00 1.11e-01 1.32e+01 ... (remaining 15168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 6231 17.00 - 34.00: 410 34.00 - 51.01: 98 51.01 - 68.01: 22 68.01 - 85.01: 4 Dihedral angle restraints: 6765 sinusoidal: 2719 harmonic: 4046 Sorted by residual: dihedral pdb=" CA SER A 798 " pdb=" C SER A 798 " pdb=" N PRO A 799 " pdb=" CA PRO A 799 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASP A 796 " pdb=" C ASP A 796 " pdb=" N HIS A 797 " pdb=" CA HIS A 797 " ideal model delta harmonic sigma weight residual -180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TYR C 702 " pdb=" C TYR C 702 " pdb=" N SER C 703 " pdb=" CA SER C 703 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 6762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1466 0.065 - 0.129: 201 0.129 - 0.194: 2 0.194 - 0.258: 0 0.258 - 0.322: 1 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CA 86N A 860 " pdb=" N 86N A 860 " pdb=" C 86N A 860 " pdb=" CB 86N A 860 " both_signs ideal model delta sigma weight residual False 2.61 2.28 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR C 493 " pdb=" N THR C 493 " pdb=" C THR C 493 " pdb=" CB THR C 493 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA ILE C 482 " pdb=" N ILE C 482 " pdb=" C ILE C 482 " pdb=" CB ILE C 482 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1667 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 66 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 67 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 320 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 581 " 0.025 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 582 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.021 5.00e-02 4.00e+02 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 188 2.65 - 3.22: 10534 3.22 - 3.78: 17065 3.78 - 4.34: 24667 4.34 - 4.90: 39870 Nonbonded interactions: 92324 Sorted by model distance: nonbonded pdb=" OG SER C 220 " pdb=" OD1 ASP C 793 " model vdw 2.092 2.440 nonbonded pdb=" OG SER C 399 " pdb=" OD2 ASP C 473 " model vdw 2.126 2.440 nonbonded pdb=" O GLY A 434 " pdb=" OG1 THR A 438 " model vdw 2.190 2.440 nonbonded pdb=" OD1 ASP A 339 " pdb=" OH TYR A 350 " model vdw 2.200 2.440 nonbonded pdb=" O SER A 771 " pdb=" OG1 THR A 775 " model vdw 2.217 2.440 ... (remaining 92319 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 5.010 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.640 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.007 0.255 11221 Z= 0.468 Angle : 0.800 47.273 15173 Z= 0.373 Chirality : 0.044 0.322 1670 Planarity : 0.004 0.048 1965 Dihedral : 12.408 85.010 4149 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.41 % Allowed : 6.91 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.20), residues: 1364 helix: -1.14 (0.17), residues: 687 sheet: -2.15 (0.46), residues: 91 loop : -2.32 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 526 HIS 0.004 0.001 HIS C 494 PHE 0.015 0.002 PHE C 475 TYR 0.016 0.002 TYR C 443 ARG 0.004 0.001 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 514 MET cc_start: 0.7505 (ttp) cc_final: 0.6643 (ttp) REVERT: A 518 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 867 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7997 (pt) REVERT: C 403 GLN cc_start: 0.7507 (tt0) cc_final: 0.7303 (tt0) REVERT: C 411 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8235 (mmmt) REVERT: C 459 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7038 (p0) REVERT: C 489 ASP cc_start: 0.7512 (p0) cc_final: 0.7082 (p0) REVERT: B 73 MET cc_start: 0.7339 (tpp) cc_final: 0.6879 (tpt) outliers start: 40 outliers final: 18 residues processed: 178 average time/residue: 1.3352 time to fit residues: 255.7263 Evaluate side-chains 122 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 845 TRP Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 35 optimal weight: 0.0370 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 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 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN C 153 GLN C 167 GLN C 189 ASN C 454 HIS C 670 ASN C 830 GLN B 42 GLN B 43 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11221 Z= 0.158 Angle : 0.498 9.731 15173 Z= 0.251 Chirality : 0.038 0.166 1670 Planarity : 0.004 0.044 1965 Dihedral : 6.152 57.349 1528 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.15 % Allowed : 11.76 % Favored : 85.08 % 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: -1.03 (0.22), residues: 1364 helix: 0.27 (0.19), residues: 705 sheet: -1.59 (0.47), residues: 93 loop : -1.71 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 635 HIS 0.004 0.001 HIS C 492 PHE 0.033 0.001 PHE A 309 TYR 0.012 0.001 TYR C 702 ARG 0.006 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8399 (mptp) cc_final: 0.7846 (mttp) REVERT: A 514 MET cc_start: 0.7628 (ttp) cc_final: 0.6824 (ttp) REVERT: A 518 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 870 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6598 (p0) REVERT: A 885 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: C 459 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6833 (p0) REVERT: C 483 MET cc_start: 0.7951 (ptm) cc_final: 0.7647 (ptm) outliers start: 37 outliers final: 15 residues processed: 140 average time/residue: 1.3929 time to fit residues: 209.6348 Evaluate side-chains 121 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN A 818 ASN B 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11221 Z= 0.160 Angle : 0.492 8.760 15173 Z= 0.247 Chirality : 0.038 0.157 1670 Planarity : 0.003 0.042 1965 Dihedral : 5.328 56.676 1513 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.67 % Allowed : 12.87 % Favored : 83.46 % 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: -0.32 (0.23), residues: 1364 helix: 0.86 (0.19), residues: 704 sheet: -1.08 (0.48), residues: 93 loop : -1.42 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 277 HIS 0.003 0.001 HIS C 800 PHE 0.016 0.001 PHE A 309 TYR 0.012 0.001 TYR C 443 ARG 0.007 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 115 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 514 MET cc_start: 0.7794 (ttp) cc_final: 0.6979 (ttp) REVERT: A 518 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 870 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6900 (p0) REVERT: A 885 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: C 459 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6807 (p0) REVERT: C 489 ASP cc_start: 0.7388 (p0) cc_final: 0.6997 (p0) REVERT: B 8 GLU cc_start: 0.7051 (tp30) cc_final: 0.6683 (tm-30) outliers start: 43 outliers final: 20 residues processed: 141 average time/residue: 1.3509 time to fit residues: 205.4147 Evaluate side-chains 126 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 32 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11221 Z= 0.183 Angle : 0.500 9.284 15173 Z= 0.250 Chirality : 0.039 0.158 1670 Planarity : 0.003 0.041 1965 Dihedral : 5.239 56.249 1512 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.01 % Allowed : 13.55 % Favored : 82.44 % 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: -0.01 (0.23), residues: 1364 helix: 1.09 (0.20), residues: 706 sheet: -0.82 (0.49), residues: 93 loop : -1.27 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 277 HIS 0.003 0.001 HIS C 800 PHE 0.015 0.001 PHE C 475 TYR 0.012 0.001 TYR C 443 ARG 0.008 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 514 MET cc_start: 0.7839 (ttp) cc_final: 0.7049 (ttp) REVERT: A 518 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 870 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6903 (p0) REVERT: A 885 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: C 127 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7495 (ttp-110) REVERT: C 459 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6840 (p0) REVERT: C 483 MET cc_start: 0.7892 (ptm) cc_final: 0.7587 (ptm) REVERT: C 489 ASP cc_start: 0.7407 (p0) cc_final: 0.7034 (p0) REVERT: B 8 GLU cc_start: 0.7054 (tp30) cc_final: 0.6734 (tm-30) REVERT: B 37 MET cc_start: 0.8549 (mmm) cc_final: 0.8289 (mmm) REVERT: B 52 MET cc_start: 0.7430 (mmm) cc_final: 0.6831 (tpt) outliers start: 47 outliers final: 29 residues processed: 143 average time/residue: 1.2787 time to fit residues: 197.9592 Evaluate side-chains 131 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.0010 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11221 Z= 0.174 Angle : 0.486 8.795 15173 Z= 0.245 Chirality : 0.039 0.156 1670 Planarity : 0.004 0.042 1965 Dihedral : 5.136 56.494 1510 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.18 % Allowed : 13.73 % Favored : 82.10 % 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: 0.25 (0.23), residues: 1364 helix: 1.31 (0.19), residues: 704 sheet: -0.61 (0.49), residues: 93 loop : -1.17 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 549 HIS 0.003 0.001 HIS C 800 PHE 0.018 0.001 PHE C 425 TYR 0.015 0.001 TYR A 288 ARG 0.008 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.5588 (ppt170) REVERT: A 514 MET cc_start: 0.7860 (ttp) cc_final: 0.6998 (ttp) REVERT: A 518 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 870 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 885 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: C 127 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7520 (ttm110) REVERT: C 483 MET cc_start: 0.7879 (ptm) cc_final: 0.7571 (ptm) REVERT: C 489 ASP cc_start: 0.7430 (p0) cc_final: 0.7010 (p0) REVERT: B 7 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: B 32 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: B 52 MET cc_start: 0.7506 (mmm) cc_final: 0.6830 (tpt) outliers start: 49 outliers final: 26 residues processed: 141 average time/residue: 1.2745 time to fit residues: 194.1131 Evaluate side-chains 129 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11221 Z= 0.217 Angle : 0.510 7.980 15173 Z= 0.257 Chirality : 0.040 0.158 1670 Planarity : 0.004 0.044 1965 Dihedral : 5.019 56.656 1507 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.01 % Allowed : 14.41 % Favored : 81.59 % 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: 0.32 (0.23), residues: 1364 helix: 1.41 (0.19), residues: 697 sheet: -0.54 (0.50), residues: 92 loop : -1.16 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 549 HIS 0.003 0.001 HIS C 800 PHE 0.016 0.001 PHE C 475 TYR 0.013 0.001 TYR C 443 ARG 0.008 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 106 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.5584 (ppt170) REVERT: A 430 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8527 (pt0) REVERT: A 514 MET cc_start: 0.7708 (ttp) cc_final: 0.6944 (ttp) REVERT: A 518 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 870 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6898 (p0) REVERT: A 885 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: C 127 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7529 (ttm110) REVERT: C 489 ASP cc_start: 0.7431 (p0) cc_final: 0.7025 (p0) REVERT: B 7 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: B 32 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: B 52 MET cc_start: 0.7483 (mmm) cc_final: 0.7057 (tpt) outliers start: 47 outliers final: 31 residues processed: 140 average time/residue: 1.2401 time to fit residues: 187.8558 Evaluate side-chains 134 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 chunk 96 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 381 ASN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11221 Z= 0.149 Angle : 0.496 10.492 15173 Z= 0.248 Chirality : 0.038 0.157 1670 Planarity : 0.004 0.046 1965 Dihedral : 4.889 56.631 1507 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.90 % Allowed : 16.03 % Favored : 81.07 % 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: 0.54 (0.23), residues: 1364 helix: 1.56 (0.20), residues: 703 sheet: -0.29 (0.51), residues: 92 loop : -1.07 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 549 HIS 0.003 0.001 HIS C 492 PHE 0.015 0.001 PHE C 425 TYR 0.012 0.001 TYR C 443 ARG 0.009 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.5695 (ppt170) REVERT: A 514 MET cc_start: 0.7701 (ttp) cc_final: 0.6902 (ttp) REVERT: A 518 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 870 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6983 (p0) REVERT: A 885 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: C 127 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7529 (ttm110) REVERT: C 345 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7234 (mtt180) REVERT: C 403 GLN cc_start: 0.7253 (tt0) cc_final: 0.7014 (mt0) REVERT: C 489 ASP cc_start: 0.7420 (p0) cc_final: 0.6986 (p0) REVERT: B 7 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6495 (tm-30) REVERT: B 52 MET cc_start: 0.7496 (mmm) cc_final: 0.7097 (tpt) REVERT: B 72 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7755 (ttm) outliers start: 34 outliers final: 24 residues processed: 133 average time/residue: 1.2562 time to fit residues: 180.6997 Evaluate side-chains 130 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11221 Z= 0.141 Angle : 0.487 9.910 15173 Z= 0.243 Chirality : 0.038 0.151 1670 Planarity : 0.004 0.044 1965 Dihedral : 4.816 56.666 1507 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.81 % Allowed : 16.71 % Favored : 80.48 % 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 (0.23), residues: 1364 helix: 1.71 (0.20), residues: 702 sheet: -0.11 (0.52), residues: 92 loop : -0.97 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 549 HIS 0.003 0.001 HIS C 492 PHE 0.014 0.001 PHE C 475 TYR 0.011 0.001 TYR C 443 ARG 0.009 0.000 ARG C 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8673 (tpp) cc_final: 0.8451 (tpt) REVERT: A 514 MET cc_start: 0.7736 (ttp) cc_final: 0.7072 (ttp) REVERT: A 518 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 870 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6976 (p0) REVERT: A 885 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7009 (pm20) REVERT: C 127 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7567 (ttm110) REVERT: C 345 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7220 (mtt180) REVERT: C 403 GLN cc_start: 0.7241 (tt0) cc_final: 0.7036 (mt0) REVERT: C 483 MET cc_start: 0.7858 (ptm) cc_final: 0.7557 (ptm) REVERT: C 489 ASP cc_start: 0.7415 (p0) cc_final: 0.6908 (p0) REVERT: B 7 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6501 (tm-30) outliers start: 33 outliers final: 21 residues processed: 135 average time/residue: 1.3087 time to fit residues: 190.6732 Evaluate side-chains 131 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11221 Z= 0.141 Angle : 0.505 9.781 15173 Z= 0.251 Chirality : 0.038 0.176 1670 Planarity : 0.004 0.044 1965 Dihedral : 4.765 56.639 1506 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.56 % Allowed : 17.22 % Favored : 80.22 % 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: 0.83 (0.23), residues: 1364 helix: 1.77 (0.20), residues: 703 sheet: -0.04 (0.50), residues: 98 loop : -0.91 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 549 HIS 0.003 0.001 HIS C 492 PHE 0.014 0.001 PHE C 475 TYR 0.020 0.001 TYR A 288 ARG 0.009 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8633 (tpp) cc_final: 0.8422 (tpt) REVERT: A 288 TYR cc_start: 0.8655 (m-80) cc_final: 0.8056 (m-80) REVERT: A 514 MET cc_start: 0.7719 (ttp) cc_final: 0.6910 (ttp) REVERT: A 518 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 870 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6916 (p0) REVERT: A 885 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: C 127 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7573 (ttm110) REVERT: C 345 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7250 (mtt180) REVERT: C 483 MET cc_start: 0.7854 (ptm) cc_final: 0.7551 (ptm) outliers start: 30 outliers final: 20 residues processed: 132 average time/residue: 1.3595 time to fit residues: 193.4664 Evaluate side-chains 128 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 6 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 125 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11221 Z= 0.187 Angle : 0.530 9.750 15173 Z= 0.265 Chirality : 0.039 0.171 1670 Planarity : 0.004 0.044 1965 Dihedral : 4.827 57.210 1506 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.56 % Allowed : 17.48 % Favored : 79.97 % 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: 0.79 (0.23), residues: 1364 helix: 1.71 (0.20), residues: 704 sheet: -0.04 (0.50), residues: 98 loop : -0.91 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 549 HIS 0.004 0.001 HIS C 800 PHE 0.015 0.001 PHE C 475 TYR 0.020 0.001 TYR A 288 ARG 0.009 0.000 ARG C 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8303 (mptp) cc_final: 0.8059 (mttp) REVERT: A 514 MET cc_start: 0.7767 (ttp) cc_final: 0.6978 (ttp) REVERT: A 518 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 870 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6910 (p0) REVERT: A 885 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: C 127 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7576 (ttm110) REVERT: C 345 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7238 (mtt180) outliers start: 30 outliers final: 24 residues processed: 127 average time/residue: 1.2575 time to fit residues: 173.6657 Evaluate side-chains 131 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102261 restraints weight = 14195.429| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.27 r_work: 0.3020 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11221 Z= 0.272 Angle : 0.569 9.881 15173 Z= 0.284 Chirality : 0.041 0.173 1670 Planarity : 0.004 0.043 1965 Dihedral : 5.004 58.071 1506 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.47 % Allowed : 17.73 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1364 helix: 1.58 (0.19), residues: 696 sheet: -0.12 (0.51), residues: 92 loop : -0.94 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 549 HIS 0.004 0.001 HIS C 800 PHE 0.017 0.002 PHE C 475 TYR 0.020 0.001 TYR A 288 ARG 0.009 0.001 ARG C 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.77 seconds wall clock time: 73 minutes 15.38 seconds (4395.38 seconds total)