null Mon 24 Dec 07:40:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2g0t-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:40:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-parrot-noncs/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-noncs.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-noncs.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 6195 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3370 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3290 (Rfree = 0.000) for 6195 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.73 Search for helices and strands: 0 residues in 0 chains, 6332 seeds are put forward NCS extension: 0 residues added, 6332 seeds are put forward Round 1: 369 peptides, 56 chains. Longest chain 20 peptides. Score 0.405 Round 2: 422 peptides, 49 chains. Longest chain 24 peptides. Score 0.518 Round 3: 427 peptides, 50 chains. Longest chain 25 peptides. Score 0.518 Round 4: 445 peptides, 43 chains. Longest chain 36 peptides. Score 0.577 Round 5: 432 peptides, 42 chains. Longest chain 25 peptides. Score 0.568 Taking the results from Round 4 Chains 46, Residues 402, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10732 restraints for refining 5052 atoms. 9033 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3121 (Rfree = 0.000) for 5052 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 2: After refmac, R = 0.2787 (Rfree = 0.000) for 4990 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 3: After refmac, R = 0.2745 (Rfree = 0.000) for 4952 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 4: After refmac, R = 0.2656 (Rfree = 0.000) for 4933 atoms. Found 19 (23 requested) and removed 29 (11 requested) atoms. Cycle 5: After refmac, R = 0.2497 (Rfree = 0.000) for 4905 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 5108 seeds are put forward NCS extension: 53 residues added (3 deleted due to clashes), 5161 seeds are put forward Round 1: 391 peptides, 47 chains. Longest chain 27 peptides. Score 0.491 Round 2: 413 peptides, 47 chains. Longest chain 21 peptides. Score 0.518 Round 3: 418 peptides, 48 chains. Longest chain 24 peptides. Score 0.518 Round 4: 419 peptides, 46 chains. Longest chain 21 peptides. Score 0.531 Round 5: 428 peptides, 47 chains. Longest chain 26 peptides. Score 0.536 Taking the results from Round 5 Chains 47, Residues 381, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11422 restraints for refining 5058 atoms. 9945 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2982 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 4994 atoms. Found 21 (23 requested) and removed 26 (11 requested) atoms. Cycle 8: After refmac, R = 0.2267 (Rfree = 0.000) for 4957 atoms. Found 22 (23 requested) and removed 24 (11 requested) atoms. Cycle 9: After refmac, R = 0.2185 (Rfree = 0.000) for 4933 atoms. Found 12 (23 requested) and removed 21 (11 requested) atoms. Cycle 10: After refmac, R = 0.2143 (Rfree = 0.000) for 4910 atoms. Found 7 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 5083 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5106 seeds are put forward Round 1: 388 peptides, 55 chains. Longest chain 15 peptides. Score 0.438 Round 2: 425 peptides, 49 chains. Longest chain 19 peptides. Score 0.521 Round 3: 426 peptides, 46 chains. Longest chain 23 peptides. Score 0.539 Round 4: 427 peptides, 51 chains. Longest chain 22 peptides. Score 0.512 Round 5: 424 peptides, 50 chains. Longest chain 30 peptides. Score 0.514 Taking the results from Round 3 Chains 51, Residues 380, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10702 restraints for refining 5057 atoms. 9081 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2976 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 12: After refmac, R = 0.2724 (Rfree = 0.000) for 4986 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 13: After refmac, R = 0.2413 (Rfree = 0.000) for 4941 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 14: After refmac, R = 0.2412 (Rfree = 0.000) for 4915 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 15: After refmac, R = 0.2394 (Rfree = 0.000) for 4897 atoms. Found 19 (23 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 2.72 Search for helices and strands: 0 residues in 0 chains, 5102 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5124 seeds are put forward Round 1: 405 peptides, 65 chains. Longest chain 14 peptides. Score 0.400 Round 2: 430 peptides, 57 chains. Longest chain 21 peptides. Score 0.481 Round 3: 422 peptides, 60 chains. Longest chain 19 peptides. Score 0.453 Round 4: 435 peptides, 47 chains. Longest chain 24 peptides. Score 0.544 Round 5: 435 peptides, 45 chains. Longest chain 36 peptides. Score 0.555 Taking the results from Round 5 Chains 50, Residues 390, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10566 restraints for refining 5057 atoms. 8871 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3053 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 17: After refmac, R = 0.2610 (Rfree = 0.000) for 4986 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 18: After refmac, R = 0.2583 (Rfree = 0.000) for 4948 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 19: After refmac, R = 0.2468 (Rfree = 0.000) for 4912 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 20: After refmac, R = 0.2264 (Rfree = 0.000) for 4885 atoms. Found 11 (23 requested) and removed 35 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 5061 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5083 seeds are put forward Round 1: 403 peptides, 58 chains. Longest chain 27 peptides. Score 0.440 Round 2: 427 peptides, 48 chains. Longest chain 24 peptides. Score 0.529 Round 3: 448 peptides, 49 chains. Longest chain 26 peptides. Score 0.548 Round 4: 445 peptides, 48 chains. Longest chain 27 peptides. Score 0.550 Round 5: 423 peptides, 46 chains. Longest chain 24 peptides. Score 0.536 Taking the results from Round 4 Chains 52, Residues 397, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10661 restraints for refining 5056 atoms. 9054 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2905 (Rfree = 0.000) for 5056 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 22: After refmac, R = 0.2772 (Rfree = 0.000) for 4984 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 23: After refmac, R = 0.2857 (Rfree = 0.000) for 4933 atoms. Found 11 (23 requested) and removed 22 (11 requested) atoms. Cycle 24: After refmac, R = 0.2582 (Rfree = 0.000) for 4902 atoms. Found 11 (23 requested) and removed 21 (11 requested) atoms. Cycle 25: After refmac, R = 0.2645 (Rfree = 0.000) for 4883 atoms. Found 3 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 5079 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5101 seeds are put forward Round 1: 384 peptides, 61 chains. Longest chain 19 peptides. Score 0.395 Round 2: 414 peptides, 50 chains. Longest chain 29 peptides. Score 0.502 Round 3: 417 peptides, 49 chains. Longest chain 22 peptides. Score 0.511 Round 4: 426 peptides, 52 chains. Longest chain 26 peptides. Score 0.505 Round 5: 422 peptides, 52 chains. Longest chain 30 peptides. Score 0.500 Taking the results from Round 3 Chains 54, Residues 368, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10646 restraints for refining 5058 atoms. 9096 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2603 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 27: After refmac, R = 0.2445 (Rfree = 0.000) for 5018 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 28: After refmac, R = 0.2439 (Rfree = 0.000) for 4992 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 29: After refmac, R = 0.2335 (Rfree = 0.000) for 4966 atoms. Found 15 (23 requested) and removed 23 (11 requested) atoms. Cycle 30: After refmac, R = 0.2477 (Rfree = 0.000) for 4945 atoms. Found 14 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 5140 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 5170 seeds are put forward Round 1: 378 peptides, 62 chains. Longest chain 17 peptides. Score 0.380 Round 2: 409 peptides, 57 chains. Longest chain 19 peptides. Score 0.454 Round 3: 419 peptides, 49 chains. Longest chain 26 peptides. Score 0.514 Round 4: 418 peptides, 56 chains. Longest chain 23 peptides. Score 0.472 Round 5: 412 peptides, 54 chains. Longest chain 25 peptides. Score 0.476 Taking the results from Round 3 Chains 49, Residues 370, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10816 restraints for refining 5054 atoms. 9279 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2555 (Rfree = 0.000) for 5054 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 32: After refmac, R = 0.2652 (Rfree = 0.000) for 4994 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 33: After refmac, R = 0.2833 (Rfree = 0.000) for 4968 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 34: After refmac, R = 0.2829 (Rfree = 0.000) for 4944 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 35: After refmac, R = 0.2869 (Rfree = 0.000) for 4927 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 5128 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5155 seeds are put forward Round 1: 353 peptides, 56 chains. Longest chain 15 peptides. Score 0.383 Round 2: 393 peptides, 53 chains. Longest chain 23 peptides. Score 0.457 Round 3: 396 peptides, 49 chains. Longest chain 24 peptides. Score 0.485 Round 4: 407 peptides, 52 chains. Longest chain 19 peptides. Score 0.481 Round 5: 426 peptides, 56 chains. Longest chain 28 peptides. Score 0.482 Taking the results from Round 3 Chains 53, Residues 347, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10906 restraints for refining 5057 atoms. 9362 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3195 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 65 (12 requested) atoms. Cycle 37: After refmac, R = 0.2916 (Rfree = 0.000) for 4988 atoms. Found 23 (23 requested) and removed 48 (11 requested) atoms. Cycle 38: After refmac, R = 0.2797 (Rfree = 0.000) for 4951 atoms. Found 19 (23 requested) and removed 25 (11 requested) atoms. Cycle 39: After refmac, R = 0.2553 (Rfree = 0.000) for 4936 atoms. Found 10 (23 requested) and removed 21 (11 requested) atoms. Cycle 40: After refmac, R = 0.2243 (Rfree = 0.000) for 4919 atoms. Found 7 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 5108 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5129 seeds are put forward Round 1: 353 peptides, 56 chains. Longest chain 24 peptides. Score 0.383 Round 2: 383 peptides, 49 chains. Longest chain 28 peptides. Score 0.468 Round 3: 412 peptides, 45 chains. Longest chain 30 peptides. Score 0.528 Round 4: 390 peptides, 50 chains. Longest chain 20 peptides. Score 0.471 Round 5: 396 peptides, 50 chains. Longest chain 26 peptides. Score 0.479 Taking the results from Round 3 Chains 48, Residues 367, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10597 restraints for refining 5058 atoms. 8950 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3252 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 88 (12 requested) atoms. Cycle 42: After refmac, R = 0.3271 (Rfree = 0.000) for 4954 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 43: After refmac, R = 0.3058 (Rfree = 0.000) for 4927 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 44: After refmac, R = 0.3043 (Rfree = 0.000) for 4901 atoms. Found 17 (23 requested) and removed 30 (11 requested) atoms. Cycle 45: After refmac, R = 0.2835 (Rfree = 0.000) for 4884 atoms. Found 8 (23 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 2.66 Search for helices and strands: 0 residues in 0 chains, 5016 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5040 seeds are put forward Round 1: 323 peptides, 61 chains. Longest chain 13 peptides. Score 0.303 Round 2: 366 peptides, 55 chains. Longest chain 18 peptides. Score 0.408 Round 3: 381 peptides, 50 chains. Longest chain 18 peptides. Score 0.459 Round 4: 391 peptides, 56 chains. Longest chain 19 peptides. Score 0.436 Round 5: 372 peptides, 54 chains. Longest chain 19 peptides. Score 0.422 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 331, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2g0t-4_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (331 residues) following loop building 3 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10611 reflections ( 99.60 % complete ) and 11108 restraints for refining 5058 atoms. 9739 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3094 (Rfree = 0.000) for 5058 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2924 (Rfree = 0.000) for 5012 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2859 (Rfree = 0.000) for 4985 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2672 (Rfree = 0.000) for 4968 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:03:53 GMT 2018 Job finished. TimeTaking 143.47 Used memory is bytes: 21068440