Mon 24 Dec 00:42:59 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 2ich-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.4-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/2ich-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.4-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 ============================================================ Mon 24 Dec 00:43:04 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/2ich-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.4-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 532 and 0 Target number of residues in the AU: 532 Target solvent content: 0.6089 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-3.4-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: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.70 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: 29.160 3.400 Wilson plot Bfac: 56.37 10621 reflections ( 99.68 % complete ) and 0 restraints for refining 5922 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3035 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3085 (Rfree = 0.000) for 5922 atoms. Found 44 (44 requested) and removed 66 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 5982 seeds are put forward NCS extension: 0 residues added, 5982 seeds are put forward Round 1: 340 peptides, 57 chains. Longest chain 16 peptides. Score 0.432 Round 2: 422 peptides, 58 chains. Longest chain 18 peptides. Score 0.578 Round 3: 441 peptides, 58 chains. Longest chain 16 peptides. Score 0.609 Round 4: 435 peptides, 51 chains. Longest chain 23 peptides. Score 0.647 Round 5: 471 peptides, 52 chains. Longest chain 21 peptides. Score 0.690 Taking the results from Round 5 Chains 60, Residues 419, Estimated correctness of the model 55.3 % 8 chains (88 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9516 restraints for refining 4869 atoms. 7575 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2730 (Rfree = 0.000) for 4869 atoms. Found 36 (36 requested) and removed 51 (18 requested) atoms. Cycle 2: After refmac, R = 0.2611 (Rfree = 0.000) for 4797 atoms. Found 25 (36 requested) and removed 38 (18 requested) atoms. Cycle 3: After refmac, R = 0.2429 (Rfree = 0.000) for 4754 atoms. Found 13 (36 requested) and removed 29 (18 requested) atoms. Cycle 4: After refmac, R = 0.2542 (Rfree = 0.000) for 4724 atoms. Found 6 (35 requested) and removed 34 (17 requested) atoms. Cycle 5: After refmac, R = 0.2406 (Rfree = 0.000) for 4683 atoms. Found 16 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 4791 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4804 seeds are put forward Round 1: 422 peptides, 55 chains. Longest chain 18 peptides. Score 0.600 Round 2: 478 peptides, 52 chains. Longest chain 27 peptides. Score 0.699 Round 3: 459 peptides, 48 chains. Longest chain 30 peptides. Score 0.699 Round 4: 473 peptides, 49 chains. Longest chain 26 peptides. Score 0.710 Round 5: 465 peptides, 48 chains. Longest chain 26 peptides. Score 0.706 Taking the results from Round 4 Chains 50, Residues 424, Estimated correctness of the model 60.4 % 6 chains (69 residues) have been docked in sequence Building loops using Loopy2018 50 chains (424 residues) following loop building 6 chains (69 residues) in sequence following loop building ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9778 restraints for refining 4874 atoms. 7828 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2660 (Rfree = 0.000) for 4874 atoms. Found 24 (36 requested) and removed 46 (18 requested) atoms. Cycle 7: After refmac, R = 0.2533 (Rfree = 0.000) for 4825 atoms. Found 15 (35 requested) and removed 32 (18 requested) atoms. Cycle 8: After refmac, R = 0.2390 (Rfree = 0.000) for 4794 atoms. Found 6 (35 requested) and removed 32 (18 requested) atoms. Cycle 9: After refmac, R = 0.2333 (Rfree = 0.000) for 4752 atoms. Found 12 (34 requested) and removed 28 (18 requested) atoms. Cycle 10: After refmac, R = 0.2278 (Rfree = 0.000) for 4727 atoms. Found 11 (32 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 4826 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4852 seeds are put forward Round 1: 415 peptides, 52 chains. Longest chain 27 peptides. Score 0.610 Round 2: 469 peptides, 51 chains. Longest chain 30 peptides. Score 0.694 Round 3: 471 peptides, 47 chains. Longest chain 30 peptides. Score 0.719 Round 4: 468 peptides, 54 chains. Longest chain 30 peptides. Score 0.674 Round 5: 494 peptides, 52 chains. Longest chain 30 peptides. Score 0.719 Taking the results from Round 5 Chains 55, Residues 442, Estimated correctness of the model 62.6 % 7 chains (103 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 196 A and 204 A 52 chains (444 residues) following loop building 6 chains (110 residues) in sequence following loop building ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9165 restraints for refining 4874 atoms. 7053 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2725 (Rfree = 0.000) for 4874 atoms. Found 32 (32 requested) and removed 51 (18 requested) atoms. Cycle 12: After refmac, R = 0.2483 (Rfree = 0.000) for 4832 atoms. Found 20 (32 requested) and removed 39 (18 requested) atoms. Cycle 13: After refmac, R = 0.2409 (Rfree = 0.000) for 4787 atoms. Found 11 (31 requested) and removed 32 (18 requested) atoms. Cycle 14: After refmac, R = 0.2299 (Rfree = 0.000) for 4759 atoms. Found 8 (29 requested) and removed 22 (17 requested) atoms. Cycle 15: After refmac, R = 0.2276 (Rfree = 0.000) for 4742 atoms. Found 11 (29 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 4849 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 4868 seeds are put forward Round 1: 391 peptides, 62 chains. Longest chain 15 peptides. Score 0.491 Round 2: 431 peptides, 53 chains. Longest chain 22 peptides. Score 0.628 Round 3: 448 peptides, 53 chains. Longest chain 17 peptides. Score 0.653 Round 4: 431 peptides, 52 chains. Longest chain 21 peptides. Score 0.635 Round 5: 454 peptides, 52 chains. Longest chain 20 peptides. Score 0.667 Taking the results from Round 5 Chains 54, Residues 402, Estimated correctness of the model 49.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 10348 restraints for refining 4874 atoms. 8702 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2733 (Rfree = 0.000) for 4874 atoms. Found 26 (29 requested) and removed 44 (18 requested) atoms. Cycle 17: After refmac, R = 0.2499 (Rfree = 0.000) for 4829 atoms. Found 29 (29 requested) and removed 30 (18 requested) atoms. Cycle 18: After refmac, R = 0.2454 (Rfree = 0.000) for 4815 atoms. Found 22 (29 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.2403 (Rfree = 0.000) for 4792 atoms. Found 21 (29 requested) and removed 26 (18 requested) atoms. Cycle 20: After refmac, R = 0.2448 (Rfree = 0.000) for 4777 atoms. Found 27 (29 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.08 Search for helices and strands: 0 residues in 0 chains, 4868 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4888 seeds are put forward Round 1: 379 peptides, 50 chains. Longest chain 19 peptides. Score 0.565 Round 2: 400 peptides, 47 chains. Longest chain 29 peptides. Score 0.622 Round 3: 425 peptides, 48 chains. Longest chain 22 peptides. Score 0.652 Round 4: 417 peptides, 40 chains. Longest chain 24 peptides. Score 0.693 Round 5: 410 peptides, 44 chains. Longest chain 23 peptides. Score 0.658 Taking the results from Round 4 Chains 48, Residues 377, Estimated correctness of the model 56.1 % 7 chains (84 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9688 restraints for refining 4874 atoms. 7888 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2561 (Rfree = 0.000) for 4874 atoms. Found 29 (29 requested) and removed 40 (18 requested) atoms. Cycle 22: After refmac, R = 0.2295 (Rfree = 0.000) for 4848 atoms. Found 23 (29 requested) and removed 31 (18 requested) atoms. Cycle 23: After refmac, R = 0.2212 (Rfree = 0.000) for 4831 atoms. Found 13 (29 requested) and removed 22 (18 requested) atoms. Cycle 24: After refmac, R = 0.2205 (Rfree = 0.000) for 4811 atoms. Found 16 (29 requested) and removed 24 (18 requested) atoms. Cycle 25: After refmac, R = 0.2180 (Rfree = 0.000) for 4796 atoms. Found 19 (29 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 4888 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4911 seeds are put forward Round 1: 385 peptides, 56 chains. Longest chain 17 peptides. Score 0.529 Round 2: 403 peptides, 50 chains. Longest chain 20 peptides. Score 0.605 Round 3: 431 peptides, 55 chains. Longest chain 23 peptides. Score 0.614 Round 4: 424 peptides, 52 chains. Longest chain 25 peptides. Score 0.624 Round 5: 424 peptides, 50 chains. Longest chain 27 peptides. Score 0.638 Taking the results from Round 5 Chains 55, Residues 374, Estimated correctness of the model 40.6 % 7 chains (83 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9785 restraints for refining 4873 atoms. 8003 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2502 (Rfree = 0.000) for 4873 atoms. Found 29 (29 requested) and removed 36 (18 requested) atoms. Cycle 27: After refmac, R = 0.2454 (Rfree = 0.000) for 4843 atoms. Found 27 (29 requested) and removed 27 (18 requested) atoms. Cycle 28: After refmac, R = 0.2427 (Rfree = 0.000) for 4836 atoms. Found 21 (29 requested) and removed 25 (18 requested) atoms. Cycle 29: After refmac, R = 0.2281 (Rfree = 0.000) for 4827 atoms. Found 20 (29 requested) and removed 26 (18 requested) atoms. Cycle 30: After refmac, R = 0.2222 (Rfree = 0.000) for 4812 atoms. Found 19 (29 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 3.08 Search for helices and strands: 0 residues in 0 chains, 4884 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4908 seeds are put forward Round 1: 379 peptides, 61 chains. Longest chain 17 peptides. Score 0.476 Round 2: 408 peptides, 52 chains. Longest chain 27 peptides. Score 0.599 Round 3: 398 peptides, 53 chains. Longest chain 25 peptides. Score 0.575 Round 4: 409 peptides, 52 chains. Longest chain 17 peptides. Score 0.600 Round 5: 403 peptides, 50 chains. Longest chain 34 peptides. Score 0.605 Taking the results from Round 5 Chains 51, Residues 353, Estimated correctness of the model 30.3 % 7 chains (70 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9957 restraints for refining 4872 atoms. 8318 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2530 (Rfree = 0.000) for 4872 atoms. Found 20 (29 requested) and removed 40 (18 requested) atoms. Cycle 32: After refmac, R = 0.2453 (Rfree = 0.000) for 4818 atoms. Found 24 (29 requested) and removed 32 (18 requested) atoms. Cycle 33: After refmac, R = 0.2215 (Rfree = 0.000) for 4794 atoms. Found 11 (29 requested) and removed 22 (18 requested) atoms. Cycle 34: After refmac, R = 0.2300 (Rfree = 0.000) for 4778 atoms. Found 24 (29 requested) and removed 26 (18 requested) atoms. Cycle 35: After refmac, R = 0.2305 (Rfree = 0.000) for 4767 atoms. Found 29 (29 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 46 residues added (3 deleted due to clashes), 4892 seeds are put forward Round 1: 342 peptides, 50 chains. Longest chain 24 peptides. Score 0.497 Round 2: 392 peptides, 50 chains. Longest chain 20 peptides. Score 0.587 Round 3: 398 peptides, 49 chains. Longest chain 22 peptides. Score 0.604 Round 4: 385 peptides, 50 chains. Longest chain 22 peptides. Score 0.576 Round 5: 393 peptides, 53 chains. Longest chain 17 peptides. Score 0.566 Taking the results from Round 3 Chains 52, Residues 349, Estimated correctness of the model 30.0 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 10267 restraints for refining 4874 atoms. 8754 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2451 (Rfree = 0.000) for 4874 atoms. Found 29 (29 requested) and removed 34 (18 requested) atoms. Cycle 37: After refmac, R = 0.2287 (Rfree = 0.000) for 4852 atoms. Found 21 (29 requested) and removed 30 (18 requested) atoms. Cycle 38: After refmac, R = 0.2209 (Rfree = 0.000) for 4826 atoms. Found 24 (29 requested) and removed 26 (18 requested) atoms. Cycle 39: After refmac, R = 0.2141 (Rfree = 0.000) for 4810 atoms. Found 19 (29 requested) and removed 26 (18 requested) atoms. Cycle 40: After refmac, R = 0.2126 (Rfree = 0.000) for 4797 atoms. Found 17 (29 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4870 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 4899 seeds are put forward Round 1: 346 peptides, 58 chains. Longest chain 14 peptides. Score 0.436 Round 2: 370 peptides, 55 chains. Longest chain 14 peptides. Score 0.509 Round 3: 375 peptides, 54 chains. Longest chain 22 peptides. Score 0.526 Round 4: 400 peptides, 50 chains. Longest chain 25 peptides. Score 0.600 Round 5: 395 peptides, 50 chains. Longest chain 22 peptides. Score 0.592 Taking the results from Round 4 Chains 50, Residues 350, Estimated correctness of the model 28.7 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 10592 restraints for refining 4874 atoms. 9189 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2427 (Rfree = 0.000) for 4874 atoms. Found 29 (29 requested) and removed 38 (18 requested) atoms. Cycle 42: After refmac, R = 0.2245 (Rfree = 0.000) for 4846 atoms. Found 21 (29 requested) and removed 26 (18 requested) atoms. Cycle 43: After refmac, R = 0.2257 (Rfree = 0.000) for 4835 atoms. Found 25 (29 requested) and removed 25 (18 requested) atoms. Cycle 44: After refmac, R = 0.2165 (Rfree = 0.000) for 4829 atoms. Found 17 (29 requested) and removed 26 (18 requested) atoms. Cycle 45: After refmac, R = 0.2011 (Rfree = 0.000) for 4813 atoms. Found 8 (29 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 4893 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4917 seeds are put forward Round 1: 312 peptides, 55 chains. Longest chain 14 peptides. Score 0.391 Round 2: 347 peptides, 44 chains. Longest chain 18 peptides. Score 0.556 Round 3: 360 peptides, 51 chains. Longest chain 21 peptides. Score 0.523 Round 4: 356 peptides, 46 chains. Longest chain 17 peptides. Score 0.556 Round 5: 330 peptides, 47 chains. Longest chain 15 peptides. Score 0.500 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 310, Estimated correctness of the model 13.7 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (310 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10621 reflections ( 99.68 % complete ) and 10707 restraints for refining 4873 atoms. 9463 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2296 (Rfree = 0.000) for 4873 atoms. Found 0 (29 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2238 (Rfree = 0.000) for 4842 atoms. Found 0 (29 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2168 (Rfree = 0.000) for 4818 atoms. Found 0 (29 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2173 (Rfree = 0.000) for 4792 atoms. TimeTaking 63.57