null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2g0t-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-hancs ############### 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 22:23:15 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/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-hancs/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 824 and 0 Target number of residues in the AU: 824 Target solvent content: 0.6194 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-4.0-parrot-hancs.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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 1.00 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: 29.560 4.001 Wilson plot Bfac: 61.14 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 10611 reflections ( 99.60 % complete ) and 0 restraints for refining 6187 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3295 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3810 (Rfree = 0.000) for 6187 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.73 Search for helices and strands: 0 residues in 0 chains, 6344 seeds are put forward NCS extension: 0 residues added, 6344 seeds are put forward Round 1: 360 peptides, 58 chains. Longest chain 14 peptides. Score 0.380 Round 2: 417 peptides, 53 chains. Longest chain 21 peptides. Score 0.488 Round 3: 432 peptides, 47 chains. Longest chain 24 peptides. Score 0.541 Round 4: 453 peptides, 53 chains. Longest chain 22 peptides. Score 0.532 Round 5: 436 peptides, 45 chains. Longest chain 23 peptides. Score 0.557 Taking the results from Round 5 Chains 48, Residues 391, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10995 restraints for refining 5056 atoms. 9359 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3150 (Rfree = 0.000) for 5056 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 2: After refmac, R = 0.2964 (Rfree = 0.000) for 4974 atoms. Found 21 (23 requested) and removed 36 (11 requested) atoms. Cycle 3: After refmac, R = 0.2783 (Rfree = 0.000) for 4917 atoms. Found 16 (23 requested) and removed 23 (11 requested) atoms. Cycle 4: After refmac, R = 0.2765 (Rfree = 0.000) for 4897 atoms. Found 15 (23 requested) and removed 23 (11 requested) atoms. Cycle 5: After refmac, R = 0.2819 (Rfree = 0.000) for 4874 atoms. Found 13 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 5045 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5070 seeds are put forward Round 1: 396 peptides, 56 chains. Longest chain 16 peptides. Score 0.443 Round 2: 427 peptides, 49 chains. Longest chain 26 peptides. Score 0.524 Round 3: 435 peptides, 47 chains. Longest chain 34 peptides. Score 0.544 Round 4: 432 peptides, 44 chains. Longest chain 23 peptides. Score 0.557 Round 5: 443 peptides, 47 chains. Longest chain 27 peptides. Score 0.554 Taking the results from Round 4 Chains 47, Residues 388, Estimated correctness of the model 0.0 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10561 restraints for refining 5056 atoms. 8894 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3119 (Rfree = 0.000) for 5056 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 7: After refmac, R = 0.2822 (Rfree = 0.000) for 4988 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 8: After refmac, R = 0.2734 (Rfree = 0.000) for 4953 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 9: After refmac, R = 0.2623 (Rfree = 0.000) for 4928 atoms. Found 15 (23 requested) and removed 30 (11 requested) atoms. Cycle 10: After refmac, R = 0.2580 (Rfree = 0.000) for 4892 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 5087 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5111 seeds are put forward Round 1: 398 peptides, 57 chains. Longest chain 24 peptides. Score 0.439 Round 2: 425 peptides, 49 chains. Longest chain 19 peptides. Score 0.521 Round 3: 432 peptides, 45 chains. Longest chain 27 peptides. Score 0.552 Round 4: 425 peptides, 47 chains. Longest chain 24 peptides. Score 0.533 Round 5: 443 peptides, 56 chains. Longest chain 26 peptides. Score 0.503 Taking the results from Round 3 Chains 45, Residues 387, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11041 restraints for refining 5057 atoms. 9538 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2982 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 12: After refmac, R = 0.2563 (Rfree = 0.000) for 5009 atoms. Found 15 (23 requested) and removed 32 (11 requested) atoms. Cycle 13: After refmac, R = 0.2369 (Rfree = 0.000) for 4970 atoms. Found 22 (23 requested) and removed 29 (11 requested) atoms. Cycle 14: After refmac, R = 0.2303 (Rfree = 0.000) for 4946 atoms. Found 17 (23 requested) and removed 29 (11 requested) atoms. Cycle 15: After refmac, R = 0.2277 (Rfree = 0.000) for 4922 atoms. Found 10 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 5098 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 5135 seeds are put forward Round 1: 395 peptides, 52 chains. Longest chain 21 peptides. Score 0.466 Round 2: 431 peptides, 51 chains. Longest chain 23 peptides. Score 0.517 Round 3: 415 peptides, 51 chains. Longest chain 20 peptides. Score 0.497 Round 4: 428 peptides, 46 chains. Longest chain 27 peptides. Score 0.542 Round 5: 411 peptides, 47 chains. Longest chain 22 peptides. Score 0.516 Taking the results from Round 4 Chains 47, Residues 382, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10740 restraints for refining 5057 atoms. 9147 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2703 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 17: After refmac, R = 0.2557 (Rfree = 0.000) for 4993 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 18: After refmac, R = 0.2471 (Rfree = 0.000) for 4957 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 19: After refmac, R = 0.2358 (Rfree = 0.000) for 4933 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 20: After refmac, R = 0.2298 (Rfree = 0.000) for 4910 atoms. Found 13 (23 requested) and removed 38 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 2.66 Search for helices and strands: 0 residues in 0 chains, 5082 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5107 seeds are put forward Round 1: 385 peptides, 60 chains. Longest chain 15 peptides. Score 0.403 Round 2: 429 peptides, 52 chains. Longest chain 21 peptides. Score 0.509 Round 3: 420 peptides, 52 chains. Longest chain 20 peptides. Score 0.498 Round 4: 416 peptides, 48 chains. Longest chain 21 peptides. Score 0.516 Round 5: 415 peptides, 51 chains. Longest chain 23 peptides. Score 0.497 Taking the results from Round 4 Chains 48, Residues 368, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10786 restraints for refining 5057 atoms. 9243 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2721 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 22: After refmac, R = 0.2518 (Rfree = 0.000) for 5011 atoms. Found 21 (23 requested) and removed 39 (11 requested) atoms. Cycle 23: After refmac, R = 0.2431 (Rfree = 0.000) for 4962 atoms. Found 18 (23 requested) and removed 33 (11 requested) atoms. Cycle 24: After refmac, R = 0.2259 (Rfree = 0.000) for 4931 atoms. Found 8 (23 requested) and removed 31 (11 requested) atoms. Cycle 25: After refmac, R = 0.2217 (Rfree = 0.000) for 4902 atoms. Found 4 (23 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 5058 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 5070 seeds are put forward Round 1: 365 peptides, 58 chains. Longest chain 17 peptides. Score 0.387 Round 2: 402 peptides, 48 chains. Longest chain 28 peptides. Score 0.499 Round 3: 395 peptides, 53 chains. Longest chain 18 peptides. Score 0.460 Round 4: 411 peptides, 54 chains. Longest chain 22 peptides. Score 0.475 Round 5: 409 peptides, 52 chains. Longest chain 24 peptides. Score 0.484 Taking the results from Round 2 Chains 51, Residues 354, Estimated correctness of the model 0.0 % 6 chains (67 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10533 restraints for refining 5056 atoms. 8907 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2657 (Rfree = 0.000) for 5056 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 27: After refmac, R = 0.2455 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Cycle 28: After refmac, R = 0.2376 (Rfree = 0.000) for 4980 atoms. Found 18 (23 requested) and removed 37 (11 requested) atoms. Cycle 29: After refmac, R = 0.2290 (Rfree = 0.000) for 4946 atoms. Found 13 (23 requested) and removed 32 (11 requested) atoms. Cycle 30: After refmac, R = 0.2222 (Rfree = 0.000) for 4915 atoms. Found 10 (23 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 5100 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5116 seeds are put forward Round 1: 375 peptides, 66 chains. Longest chain 13 peptides. Score 0.350 Round 2: 417 peptides, 59 chains. Longest chain 14 peptides. Score 0.453 Round 3: 401 peptides, 52 chains. Longest chain 29 peptides. Score 0.474 Round 4: 417 peptides, 53 chains. Longest chain 23 peptides. Score 0.488 Round 5: 412 peptides, 57 chains. Longest chain 21 peptides. Score 0.458 Taking the results from Round 4 Chains 57, Residues 364, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10732 restraints for refining 5055 atoms. 9231 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3194 (Rfree = 0.000) for 5055 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 32: After refmac, R = 0.3015 (Rfree = 0.000) for 5006 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 33: After refmac, R = 0.2780 (Rfree = 0.000) for 4971 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 34: After refmac, R = 0.2450 (Rfree = 0.000) for 4944 atoms. Found 9 (23 requested) and removed 26 (11 requested) atoms. Cycle 35: After refmac, R = 0.2724 (Rfree = 0.000) for 4917 atoms. Found 6 (23 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 5092 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5110 seeds are put forward Round 1: 350 peptides, 56 chains. Longest chain 14 peptides. Score 0.378 Round 2: 360 peptides, 53 chains. Longest chain 16 peptides. Score 0.412 Round 3: 390 peptides, 54 chains. Longest chain 18 peptides. Score 0.447 Round 4: 407 peptides, 52 chains. Longest chain 23 peptides. Score 0.481 Round 5: 397 peptides, 52 chains. Longest chain 33 peptides. Score 0.468 Taking the results from Round 4 Chains 52, Residues 355, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11284 restraints for refining 5057 atoms. 9885 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3071 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 37: After refmac, R = 0.2733 (Rfree = 0.000) for 5023 atoms. Found 15 (24 requested) and removed 25 (12 requested) atoms. Cycle 38: After refmac, R = 0.2887 (Rfree = 0.000) for 4991 atoms. Found 15 (23 requested) and removed 25 (11 requested) atoms. Cycle 39: After refmac, R = 0.2823 (Rfree = 0.000) for 4969 atoms. Found 12 (23 requested) and removed 28 (11 requested) atoms. Cycle 40: After refmac, R = 0.2281 (Rfree = 0.000) for 4944 atoms. Found 5 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 5102 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 5132 seeds are put forward Round 1: 366 peptides, 63 chains. Longest chain 15 peptides. Score 0.356 Round 2: 396 peptides, 55 chains. Longest chain 19 peptides. Score 0.449 Round 3: 394 peptides, 53 chains. Longest chain 17 peptides. Score 0.458 Round 4: 404 peptides, 54 chains. Longest chain 22 peptides. Score 0.466 Round 5: 386 peptides, 55 chains. Longest chain 18 peptides. Score 0.435 Taking the results from Round 4 Chains 56, Residues 350, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10872 restraints for refining 5057 atoms. 9405 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3108 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 42: After refmac, R = 0.2606 (Rfree = 0.000) for 5023 atoms. Found 12 (24 requested) and removed 28 (12 requested) atoms. Cycle 43: After refmac, R = 0.2690 (Rfree = 0.000) for 4989 atoms. Found 10 (23 requested) and removed 22 (11 requested) atoms. Cycle 44: After refmac, R = 0.2741 (Rfree = 0.000) for 4962 atoms. Found 8 (23 requested) and removed 24 (11 requested) atoms. Cycle 45: After refmac, R = 0.2769 (Rfree = 0.000) for 4935 atoms. Found 7 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 5093 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5114 seeds are put forward Round 1: 330 peptides, 63 chains. Longest chain 10 peptides. Score 0.301 Round 2: 367 peptides, 53 chains. Longest chain 14 peptides. Score 0.422 Round 3: 380 peptides, 52 chains. Longest chain 20 peptides. Score 0.446 Round 4: 393 peptides, 50 chains. Longest chain 20 peptides. Score 0.475 Round 5: 404 peptides, 49 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 355, 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 2g0t-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10611 reflections ( 99.60 % complete ) and 11261 restraints for refining 5058 atoms. 9890 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2677 (Rfree = 0.000) for 5058 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2664 (Rfree = 0.000) for 5025 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2921 (Rfree = 0.000) for 4993 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2469 (Rfree = 0.000) for 4976 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:56:06 GMT 2018 Job finished. TimeTaking 153.02 Used memory is bytes: 7875080