null Sun 23 Dec 23:49:38 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hx1-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 23:49:43 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 800 and 0 Target number of residues in the AU: 800 Target solvent content: 0.6349 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-4.0-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 93.753 4.000 Wilson plot Bfac: 69.10 10515 reflections ( 99.59 % complete ) and 0 restraints for refining 10061 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3455 (Rfree = 0.000) for 10061 atoms. Found 47 (47 requested) and removed 197 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 10004 seeds are put forward NCS extension: 0 residues added, 10004 seeds are put forward Round 1: 310 peptides, 69 chains. Longest chain 10 peptides. Score 0.226 Round 2: 452 peptides, 89 chains. Longest chain 12 peptides. Score 0.317 Round 3: 519 peptides, 97 chains. Longest chain 12 peptides. Score 0.364 Round 4: 527 peptides, 91 chains. Longest chain 12 peptides. Score 0.410 Round 5: 529 peptides, 89 chains. Longest chain 12 peptides. Score 0.424 Taking the results from Round 5 Chains 89, Residues 440, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19389 restraints for refining 8207 atoms. 17718 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3608 (Rfree = 0.000) for 8207 atoms. Found 38 (38 requested) and removed 83 (19 requested) atoms. Cycle 2: After refmac, R = 0.3388 (Rfree = 0.000) for 8028 atoms. Found 38 (38 requested) and removed 104 (19 requested) atoms. Cycle 3: After refmac, R = 0.3377 (Rfree = 0.000) for 7898 atoms. Found 37 (37 requested) and removed 69 (18 requested) atoms. Cycle 4: After refmac, R = 0.2364 (Rfree = 0.000) for 7825 atoms. Found 23 (37 requested) and removed 47 (18 requested) atoms. Cycle 5: After refmac, R = 0.2052 (Rfree = 0.000) for 7775 atoms. Found 18 (37 requested) and removed 48 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 8024 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8039 seeds are put forward Round 1: 480 peptides, 95 chains. Longest chain 9 peptides. Score 0.321 Round 2: 552 peptides, 91 chains. Longest chain 19 peptides. Score 0.442 Round 3: 552 peptides, 88 chains. Longest chain 16 peptides. Score 0.459 Round 4: 568 peptides, 88 chains. Longest chain 19 peptides. Score 0.479 Round 5: 587 peptides, 87 chains. Longest chain 17 peptides. Score 0.507 Taking the results from Round 5 Chains 87, Residues 500, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19003 restraints for refining 8206 atoms. 17080 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2619 (Rfree = 0.000) for 8206 atoms. Found 38 (38 requested) and removed 74 (19 requested) atoms. Cycle 7: After refmac, R = 0.2584 (Rfree = 0.000) for 8086 atoms. Found 38 (38 requested) and removed 77 (19 requested) atoms. Cycle 8: After refmac, R = 0.2850 (Rfree = 0.000) for 8000 atoms. Found 38 (38 requested) and removed 105 (19 requested) atoms. Cycle 9: After refmac, R = 0.1814 (Rfree = 0.000) for 7908 atoms. Found 23 (37 requested) and removed 36 (18 requested) atoms. Cycle 10: After refmac, R = 0.1595 (Rfree = 0.000) for 7884 atoms. Found 8 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 8142 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 8158 seeds are put forward Round 1: 473 peptides, 96 chains. Longest chain 13 peptides. Score 0.305 Round 2: 547 peptides, 87 chains. Longest chain 18 peptides. Score 0.458 Round 3: 585 peptides, 92 chains. Longest chain 19 peptides. Score 0.478 Round 4: 559 peptides, 81 chains. Longest chain 15 peptides. Score 0.505 Round 5: 579 peptides, 83 chains. Longest chain 19 peptides. Score 0.518 Taking the results from Round 5 Chains 83, Residues 496, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18817 restraints for refining 8208 atoms. 16904 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2968 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 234 (19 requested) atoms. Cycle 12: After refmac, R = 0.2735 (Rfree = 0.000) for 7951 atoms. Found 38 (38 requested) and removed 59 (19 requested) atoms. Cycle 13: After refmac, R = 0.2646 (Rfree = 0.000) for 7879 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 14: After refmac, R = 0.2298 (Rfree = 0.000) for 7836 atoms. Found 18 (37 requested) and removed 64 (18 requested) atoms. Cycle 15: After refmac, R = 0.1706 (Rfree = 0.000) for 7773 atoms. Found 20 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 7991 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 8011 seeds are put forward Round 1: 470 peptides, 92 chains. Longest chain 11 peptides. Score 0.325 Round 2: 536 peptides, 89 chains. Longest chain 12 peptides. Score 0.433 Round 3: 540 peptides, 85 chains. Longest chain 16 peptides. Score 0.460 Round 4: 562 peptides, 82 chains. Longest chain 16 peptides. Score 0.503 Round 5: 577 peptides, 84 chains. Longest chain 19 peptides. Score 0.510 Taking the results from Round 5 Chains 84, Residues 493, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19142 restraints for refining 8208 atoms. 17254 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2969 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 81 (19 requested) atoms. Cycle 17: After refmac, R = 0.2545 (Rfree = 0.000) for 8114 atoms. Found 38 (38 requested) and removed 82 (19 requested) atoms. Cycle 18: After refmac, R = 0.2650 (Rfree = 0.000) for 8025 atoms. Found 38 (38 requested) and removed 154 (19 requested) atoms. Cycle 19: After refmac, R = 0.2097 (Rfree = 0.000) for 7870 atoms. Found 33 (37 requested) and removed 31 (18 requested) atoms. Cycle 20: After refmac, R = 0.1775 (Rfree = 0.000) for 7855 atoms. Found 10 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 8090 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8107 seeds are put forward Round 1: 492 peptides, 94 chains. Longest chain 13 peptides. Score 0.344 Round 2: 516 peptides, 84 chains. Longest chain 14 peptides. Score 0.435 Round 3: 543 peptides, 81 chains. Longest chain 21 peptides. Score 0.486 Round 4: 566 peptides, 85 chains. Longest chain 16 peptides. Score 0.492 Round 5: 566 peptides, 84 chains. Longest chain 30 peptides. Score 0.497 Taking the results from Round 5 Chains 86, Residues 482, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18636 restraints for refining 8208 atoms. 16721 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3040 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 22: After refmac, R = 0.2512 (Rfree = 0.000) for 8136 atoms. Found 38 (38 requested) and removed 45 (19 requested) atoms. Cycle 23: After refmac, R = 0.2266 (Rfree = 0.000) for 8066 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 24: After refmac, R = 0.1860 (Rfree = 0.000) for 8016 atoms. Found 17 (38 requested) and removed 36 (19 requested) atoms. Cycle 25: After refmac, R = 0.1645 (Rfree = 0.000) for 7967 atoms. Found 10 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 8156 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 8179 seeds are put forward Round 1: 471 peptides, 91 chains. Longest chain 13 peptides. Score 0.332 Round 2: 517 peptides, 89 chains. Longest chain 15 peptides. Score 0.408 Round 3: 531 peptides, 85 chains. Longest chain 15 peptides. Score 0.449 Round 4: 539 peptides, 82 chains. Longest chain 16 peptides. Score 0.475 Round 5: 531 peptides, 80 chains. Longest chain 26 peptides. Score 0.476 Taking the results from Round 5 Chains 80, Residues 451, Estimated correctness of the model 0.0 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18611 restraints for refining 8205 atoms. 16711 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2995 (Rfree = 0.000) for 8205 atoms. Found 38 (38 requested) and removed 79 (19 requested) atoms. Cycle 27: After refmac, R = 0.2529 (Rfree = 0.000) for 8091 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 28: After refmac, R = 0.2670 (Rfree = 0.000) for 8043 atoms. Found 38 (38 requested) and removed 65 (19 requested) atoms. Cycle 29: After refmac, R = 0.1907 (Rfree = 0.000) for 7982 atoms. Found 25 (38 requested) and removed 30 (19 requested) atoms. Cycle 30: After refmac, R = 0.1722 (Rfree = 0.000) for 7963 atoms. Found 11 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8152 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8175 seeds are put forward Round 1: 429 peptides, 89 chains. Longest chain 9 peptides. Score 0.283 Round 2: 463 peptides, 85 chains. Longest chain 15 peptides. Score 0.357 Round 3: 468 peptides, 79 chains. Longest chain 12 peptides. Score 0.400 Round 4: 461 peptides, 76 chains. Longest chain 17 peptides. Score 0.408 Round 5: 455 peptides, 77 chains. Longest chain 16 peptides. Score 0.394 Taking the results from Round 4 Chains 76, Residues 385, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19433 restraints for refining 8207 atoms. 17969 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2635 (Rfree = 0.000) for 8207 atoms. Found 38 (38 requested) and removed 60 (19 requested) atoms. Cycle 32: After refmac, R = 0.2591 (Rfree = 0.000) for 8138 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 33: After refmac, R = 0.2639 (Rfree = 0.000) for 8092 atoms. Found 38 (38 requested) and removed 78 (19 requested) atoms. Cycle 34: After refmac, R = 0.1982 (Rfree = 0.000) for 8023 atoms. Found 14 (38 requested) and removed 35 (19 requested) atoms. Cycle 35: After refmac, R = 0.1662 (Rfree = 0.000) for 7983 atoms. Found 11 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8163 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 8188 seeds are put forward Round 1: 431 peptides, 92 chains. Longest chain 9 peptides. Score 0.267 Round 2: 462 peptides, 85 chains. Longest chain 15 peptides. Score 0.356 Round 3: 487 peptides, 84 chains. Longest chain 15 peptides. Score 0.396 Round 4: 476 peptides, 88 chains. Longest chain 13 peptides. Score 0.357 Round 5: 505 peptides, 81 chains. Longest chain 20 peptides. Score 0.438 Taking the results from Round 5 Chains 81, Residues 424, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19231 restraints for refining 8208 atoms. 17616 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2840 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 57 (19 requested) atoms. Cycle 37: After refmac, R = 0.2351 (Rfree = 0.000) for 8133 atoms. Found 38 (38 requested) and removed 197 (19 requested) atoms. Cycle 38: After refmac, R = 0.2213 (Rfree = 0.000) for 7948 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. Cycle 39: After refmac, R = 0.1817 (Rfree = 0.000) for 7911 atoms. Found 16 (37 requested) and removed 30 (18 requested) atoms. Cycle 40: After refmac, R = 0.1854 (Rfree = 0.000) for 7871 atoms. Found 14 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 8012 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 8036 seeds are put forward Round 1: 350 peptides, 74 chains. Longest chain 10 peptides. Score 0.257 Round 2: 391 peptides, 69 chains. Longest chain 14 peptides. Score 0.353 Round 3: 405 peptides, 71 chains. Longest chain 12 peptides. Score 0.360 Round 4: 418 peptides, 74 chains. Longest chain 19 peptides. Score 0.360 Round 5: 409 peptides, 72 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 5 Chains 72, Residues 337, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19581 restraints for refining 8174 atoms. 18292 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2600 (Rfree = 0.000) for 8174 atoms. Found 38 (38 requested) and removed 45 (19 requested) atoms. Cycle 42: After refmac, R = 0.2568 (Rfree = 0.000) for 8103 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 43: After refmac, R = 0.2516 (Rfree = 0.000) for 8047 atoms. Found 38 (38 requested) and removed 39 (19 requested) atoms. Cycle 44: After refmac, R = 0.1995 (Rfree = 0.000) for 8002 atoms. Found 23 (38 requested) and removed 33 (19 requested) atoms. Cycle 45: After refmac, R = 0.1781 (Rfree = 0.000) for 7973 atoms. Found 15 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 8119 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8134 seeds are put forward Round 1: 297 peptides, 66 chains. Longest chain 8 peptides. Score 0.225 Round 2: 332 peptides, 64 chains. Longest chain 11 peptides. Score 0.296 Round 3: 360 peptides, 69 chains. Longest chain 9 peptides. Score 0.306 Round 4: 368 peptides, 66 chains. Longest chain 10 peptides. Score 0.338 Round 5: 367 peptides, 67 chains. Longest chain 14 peptides. Score 0.330 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 302, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hx1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10515 reflections ( 99.59 % complete ) and 18784 restraints for refining 7947 atoms. 17642 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2531 (Rfree = 0.000) for 7947 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2519 (Rfree = 0.000) for 7901 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2539 (Rfree = 0.000) for 7854 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2373 (Rfree = 0.000) for 7808 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:17:27 GMT 2018 Job finished. TimeTaking 87.81 Used memory is bytes: 11186904