Mon 24 Dec 00:08:19 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 2it9-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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/2it9-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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 00:08:24 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/2it9-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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 418 and 0 Target number of residues in the AU: 418 Target solvent content: 0.6240 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.2-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: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 3.200 Wilson plot Bfac: 63.35 10303 reflections ( 98.61 % complete ) and 0 restraints for refining 4548 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3366 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2737 (Rfree = 0.000) for 4548 atoms. Found 40 (40 requested) and removed 36 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 4644 seeds are put forward NCS extension: 0 residues added, 4644 seeds are put forward Round 1: 264 peptides, 40 chains. Longest chain 13 peptides. Score 0.469 Round 2: 338 peptides, 42 chains. Longest chain 22 peptides. Score 0.612 Round 3: 358 peptides, 41 chains. Longest chain 24 peptides. Score 0.657 Round 4: 355 peptides, 41 chains. Longest chain 22 peptides. Score 0.652 Round 5: 376 peptides, 39 chains. Longest chain 24 peptides. Score 0.702 Taking the results from Round 5 Chains 41, Residues 337, Estimated correctness of the model 65.6 % 4 chains (54 residues) have been docked in sequence Building loops using Loopy2018 41 chains (337 residues) following loop building 4 chains (54 residues) in sequence following loop building ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7078 restraints for refining 3709 atoms. 5536 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2739 (Rfree = 0.000) for 3709 atoms. Found 33 (33 requested) and removed 35 (16 requested) atoms. Cycle 2: After refmac, R = 0.2508 (Rfree = 0.000) for 3679 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 3: After refmac, R = 0.2433 (Rfree = 0.000) for 3660 atoms. Found 16 (31 requested) and removed 22 (16 requested) atoms. Cycle 4: After refmac, R = 0.2382 (Rfree = 0.000) for 3645 atoms. Found 16 (30 requested) and removed 18 (16 requested) atoms. Cycle 5: After refmac, R = 0.2293 (Rfree = 0.000) for 3640 atoms. Found 17 (29 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3797 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3820 seeds are put forward Round 1: 344 peptides, 42 chains. Longest chain 27 peptides. Score 0.623 Round 2: 380 peptides, 40 chains. Longest chain 25 peptides. Score 0.701 Round 3: 394 peptides, 36 chains. Longest chain 30 peptides. Score 0.748 Round 4: 394 peptides, 30 chains. Longest chain 42 peptides. Score 0.784 Round 5: 390 peptides, 34 chains. Longest chain 36 peptides. Score 0.755 Taking the results from Round 4 Chains 31, Residues 364, Estimated correctness of the model 80.9 % 3 chains (86 residues) have been docked in sequence Building loops using Loopy2018 31 chains (364 residues) following loop building 3 chains (86 residues) in sequence following loop building ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 6667 restraints for refining 3710 atoms. 4870 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2693 (Rfree = 0.000) for 3710 atoms. Found 30 (30 requested) and removed 32 (16 requested) atoms. Cycle 7: After refmac, R = 0.2520 (Rfree = 0.000) for 3687 atoms. Found 15 (29 requested) and removed 24 (16 requested) atoms. Cycle 8: After refmac, R = 0.2417 (Rfree = 0.000) for 3669 atoms. Found 15 (28 requested) and removed 18 (16 requested) atoms. Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 3660 atoms. Found 9 (27 requested) and removed 16 (16 requested) atoms. Cycle 10: After refmac, R = 0.2332 (Rfree = 0.000) for 3647 atoms. Found 9 (26 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 41 residues added (17 deleted due to clashes), 3787 seeds are put forward Round 1: 347 peptides, 43 chains. Longest chain 16 peptides. Score 0.620 Round 2: 378 peptides, 39 chains. Longest chain 23 peptides. Score 0.705 Round 3: 388 peptides, 37 chains. Longest chain 37 peptides. Score 0.733 Round 4: 377 peptides, 40 chains. Longest chain 22 peptides. Score 0.696 Round 5: 385 peptides, 34 chains. Longest chain 30 peptides. Score 0.748 Taking the results from Round 5 Chains 37, Residues 351, Estimated correctness of the model 74.7 % 6 chains (112 residues) have been docked in sequence Building loops using Loopy2018 37 chains (351 residues) following loop building 6 chains (112 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 10303 reflections ( 98.61 % complete ) and 6472 restraints for refining 3710 atoms. 4626 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2912 (Rfree = 0.000) for 3710 atoms. Found 26 (26 requested) and removed 35 (16 requested) atoms. Cycle 12: After refmac, R = 0.2468 (Rfree = 0.000) for 3672 atoms. Found 26 (26 requested) and removed 21 (16 requested) atoms. Cycle 13: After refmac, R = 0.2360 (Rfree = 0.000) for 3661 atoms. Found 11 (24 requested) and removed 22 (16 requested) atoms. Cycle 14: After refmac, R = 0.2360 (Rfree = 0.000) for 3641 atoms. Found 18 (24 requested) and removed 16 (16 requested) atoms. Cycle 15: After refmac, R = 0.2312 (Rfree = 0.000) for 3637 atoms. Found 23 (23 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 3770 seeds are put forward Round 1: 347 peptides, 42 chains. Longest chain 29 peptides. Score 0.629 Round 2: 373 peptides, 32 chains. Longest chain 36 peptides. Score 0.745 Round 3: 368 peptides, 38 chains. Longest chain 32 peptides. Score 0.696 Round 4: 375 peptides, 34 chains. Longest chain 35 peptides. Score 0.735 Round 5: 366 peptides, 35 chains. Longest chain 36 peptides. Score 0.715 Taking the results from Round 2 Chains 35, Residues 341, Estimated correctness of the model 74.1 % 3 chains (67 residues) have been docked in sequence Building loops using Loopy2018 35 chains (341 residues) following loop building 3 chains (67 residues) in sequence following loop building ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 6947 restraints for refining 3710 atoms. 5312 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2662 (Rfree = 0.000) for 3710 atoms. Found 23 (23 requested) and removed 26 (16 requested) atoms. Cycle 17: After refmac, R = 0.2514 (Rfree = 0.000) for 3697 atoms. Found 22 (22 requested) and removed 21 (16 requested) atoms. Cycle 18: After refmac, R = 0.2368 (Rfree = 0.000) for 3692 atoms. Found 18 (22 requested) and removed 23 (16 requested) atoms. Cycle 19: After refmac, R = 0.2195 (Rfree = 0.000) for 3683 atoms. Found 8 (21 requested) and removed 21 (16 requested) atoms. Cycle 20: After refmac, R = 0.2258 (Rfree = 0.000) for 3662 atoms. Found 20 (20 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 24 residues added (7 deleted due to clashes), 3795 seeds are put forward Round 1: 335 peptides, 37 chains. Longest chain 30 peptides. Score 0.649 Round 2: 362 peptides, 42 chains. Longest chain 22 peptides. Score 0.656 Round 3: 361 peptides, 38 chains. Longest chain 36 peptides. Score 0.685 Round 4: 348 peptides, 37 chains. Longest chain 24 peptides. Score 0.671 Round 5: 334 peptides, 42 chains. Longest chain 21 peptides. Score 0.604 Taking the results from Round 3 Chains 41, Residues 323, Estimated correctness of the model 61.9 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7308 restraints for refining 3709 atoms. 5904 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2394 (Rfree = 0.000) for 3709 atoms. Found 20 (20 requested) and removed 24 (16 requested) atoms. Cycle 22: After refmac, R = 0.2341 (Rfree = 0.000) for 3696 atoms. Found 20 (20 requested) and removed 22 (16 requested) atoms. Cycle 23: After refmac, R = 0.2246 (Rfree = 0.000) for 3691 atoms. Found 15 (20 requested) and removed 16 (16 requested) atoms. Cycle 24: After refmac, R = 0.2181 (Rfree = 0.000) for 3685 atoms. Found 12 (20 requested) and removed 17 (16 requested) atoms. Cycle 25: After refmac, R = 0.2143 (Rfree = 0.000) for 3679 atoms. Found 7 (20 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 3767 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 3784 seeds are put forward Round 1: 320 peptides, 39 chains. Longest chain 31 peptides. Score 0.603 Round 2: 332 peptides, 36 chains. Longest chain 32 peptides. Score 0.652 Round 3: 341 peptides, 39 chains. Longest chain 34 peptides. Score 0.643 Round 4: 329 peptides, 42 chains. Longest chain 16 peptides. Score 0.594 Round 5: 328 peptides, 39 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 2 Chains 36, Residues 296, Estimated correctness of the model 54.3 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7487 restraints for refining 3710 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2365 (Rfree = 0.000) for 3710 atoms. Found 20 (20 requested) and removed 24 (16 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2296 (Rfree = 0.000) for 3697 atoms. Found 20 (20 requested) and removed 17 (16 requested) atoms. Cycle 28: After refmac, R = 0.2265 (Rfree = 0.000) for 3691 atoms. Found 13 (20 requested) and removed 17 (16 requested) atoms. Cycle 29: After refmac, R = 0.2268 (Rfree = 0.000) for 3681 atoms. Found 13 (20 requested) and removed 16 (16 requested) atoms. Cycle 30: After refmac, R = 0.2177 (Rfree = 0.000) for 3677 atoms. Found 7 (20 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3778 seeds are put forward NCS extension: 51 residues added (12 deleted due to clashes), 3829 seeds are put forward Round 1: 290 peptides, 38 chains. Longest chain 32 peptides. Score 0.550 Round 2: 317 peptides, 36 chains. Longest chain 31 peptides. Score 0.624 Round 3: 310 peptides, 39 chains. Longest chain 21 peptides. Score 0.583 Round 4: 324 peptides, 31 chains. Longest chain 32 peptides. Score 0.678 Round 5: 315 peptides, 34 chains. Longest chain 21 peptides. Score 0.638 Taking the results from Round 4 Chains 33, Residues 293, Estimated correctness of the model 60.4 % 3 chains (60 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7175 restraints for refining 3710 atoms. 5758 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2578 (Rfree = 0.000) for 3710 atoms. Found 20 (20 requested) and removed 22 (16 requested) atoms. Cycle 32: After refmac, R = 0.2271 (Rfree = 0.000) for 3699 atoms. Found 17 (20 requested) and removed 20 (16 requested) atoms. Cycle 33: After refmac, R = 0.2163 (Rfree = 0.000) for 3694 atoms. Found 9 (20 requested) and removed 16 (16 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 3685 atoms. Found 12 (20 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.2189 (Rfree = 0.000) for 3679 atoms. Found 11 (20 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3760 seeds are put forward NCS extension: 50 residues added (9 deleted due to clashes), 3810 seeds are put forward Round 1: 283 peptides, 36 chains. Longest chain 28 peptides. Score 0.555 Round 2: 298 peptides, 33 chains. Longest chain 29 peptides. Score 0.614 Round 3: 291 peptides, 34 chains. Longest chain 31 peptides. Score 0.591 Round 4: 320 peptides, 35 chains. Longest chain 30 peptides. Score 0.638 Round 5: 327 peptides, 40 chains. Longest chain 33 peptides. Score 0.608 Taking the results from Round 4 Chains 35, Residues 285, Estimated correctness of the model 50.9 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7394 restraints for refining 3709 atoms. 6062 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2418 (Rfree = 0.000) for 3709 atoms. Found 20 (20 requested) and removed 25 (16 requested) atoms. Cycle 37: After refmac, R = 0.2275 (Rfree = 0.000) for 3694 atoms. Found 17 (20 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.2251 (Rfree = 0.000) for 3688 atoms. Found 8 (20 requested) and removed 17 (16 requested) atoms. Cycle 39: After refmac, R = 0.2150 (Rfree = 0.000) for 3678 atoms. Found 11 (20 requested) and removed 19 (16 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2168 (Rfree = 0.000) for 3668 atoms. Found 15 (19 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3783 seeds are put forward NCS extension: 31 residues added (10 deleted due to clashes), 3814 seeds are put forward Round 1: 268 peptides, 42 chains. Longest chain 21 peptides. Score 0.457 Round 2: 326 peptides, 41 chains. Longest chain 30 peptides. Score 0.597 Round 3: 323 peptides, 37 chains. Longest chain 24 peptides. Score 0.627 Round 4: 318 peptides, 37 chains. Longest chain 31 peptides. Score 0.617 Round 5: 314 peptides, 35 chains. Longest chain 29 peptides. Score 0.627 Taking the results from Round 5 Chains 35, Residues 279, Estimated correctness of the model 48.1 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7585 restraints for refining 3710 atoms. 6366 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2445 (Rfree = 0.000) for 3710 atoms. Found 20 (20 requested) and removed 22 (16 requested) atoms. Cycle 42: After refmac, R = 0.2333 (Rfree = 0.000) for 3701 atoms. Found 20 (20 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.2306 (Rfree = 0.000) for 3698 atoms. Found 16 (20 requested) and removed 16 (16 requested) atoms. Cycle 44: After refmac, R = 0.2275 (Rfree = 0.000) for 3694 atoms. Found 13 (20 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.2205 (Rfree = 0.000) for 3687 atoms. Found 20 (20 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 3811 seeds are put forward Round 1: 272 peptides, 38 chains. Longest chain 21 peptides. Score 0.510 Round 2: 293 peptides, 37 chains. Longest chain 19 peptides. Score 0.566 Round 3: 295 peptides, 33 chains. Longest chain 26 peptides. Score 0.608 Round 4: 284 peptides, 37 chains. Longest chain 21 peptides. Score 0.547 Round 5: 284 peptides, 37 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 262, Estimated correctness of the model 43.2 % 2 chains (29 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2it9-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (262 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10303 reflections ( 98.61 % complete ) and 7747 restraints for refining 3710 atoms. 6603 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2464 (Rfree = 0.000) for 3710 atoms. Found 0 (20 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2372 (Rfree = 0.000) for 3686 atoms. Found 0 (20 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2311 (Rfree = 0.000) for 3667 atoms. Found 0 (19 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2312 (Rfree = 0.000) for 3648 atoms. Found 0 (19 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 52.55