Sun 23 Dec 23:51:56 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 2a2m-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.6-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/2a2m-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.6-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 23:52:00 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/2a2m-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.6-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 617 and 0 Target number of residues in the AU: 617 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-3.6-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4128 target number of atoms Had to go as low as 0.95 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: 163.559 3.600 Wilson plot Bfac: 76.60 11808 reflections ( 99.75 % complete ) and 0 restraints for refining 4548 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3420 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2861 (Rfree = 0.000) for 4548 atoms. Found 29 (29 requested) and removed 141 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.56 Search for helices and strands: 0 residues in 0 chains, 4562 seeds are put forward NCS extension: 0 residues added, 4562 seeds are put forward Round 1: 311 peptides, 51 chains. Longest chain 20 peptides. Score 0.383 Round 2: 342 peptides, 46 chains. Longest chain 19 peptides. Score 0.473 Round 3: 354 peptides, 42 chains. Longest chain 27 peptides. Score 0.520 Round 4: 346 peptides, 41 chains. Longest chain 24 peptides. Score 0.515 Round 5: 366 peptides, 48 chains. Longest chain 24 peptides. Score 0.496 Taking the results from Round 3 Chains 49, Residues 312, Estimated correctness of the model 0.0 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7455 restraints for refining 3741 atoms. 6036 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2846 (Rfree = 0.000) for 3741 atoms. Found 24 (24 requested) and removed 42 (12 requested) atoms. Cycle 2: After refmac, R = 0.2665 (Rfree = 0.000) for 3660 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 3: After refmac, R = 0.2568 (Rfree = 0.000) for 3633 atoms. Found 21 (23 requested) and removed 20 (11 requested) atoms. Cycle 4: After refmac, R = 0.2498 (Rfree = 0.000) for 3617 atoms. Found 21 (23 requested) and removed 18 (11 requested) atoms. Cycle 5: After refmac, R = 0.2409 (Rfree = 0.000) for 3610 atoms. Found 14 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.56 Search for helices and strands: 0 residues in 0 chains, 3786 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3797 seeds are put forward Round 1: 362 peptides, 44 chains. Longest chain 29 peptides. Score 0.518 Round 2: 366 peptides, 35 chains. Longest chain 34 peptides. Score 0.584 Round 3: 370 peptides, 34 chains. Longest chain 34 peptides. Score 0.596 Round 4: 359 peptides, 38 chains. Longest chain 28 peptides. Score 0.555 Round 5: 359 peptides, 32 chains. Longest chain 29 peptides. Score 0.595 Taking the results from Round 3 Chains 38, Residues 336, Estimated correctness of the model 13.1 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11808 reflections ( 99.75 % complete ) and 7698 restraints for refining 3742 atoms. 6257 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2720 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 7: After refmac, R = 0.2510 (Rfree = 0.000) for 3710 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.2410 (Rfree = 0.000) for 3698 atoms. Found 20 (23 requested) and removed 14 (11 requested) atoms. Cycle 9: After refmac, R = 0.2362 (Rfree = 0.000) for 3685 atoms. Found 22 (23 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 3679 atoms. Found 16 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3852 seeds are put forward NCS extension: 28 residues added (9 deleted due to clashes), 3880 seeds are put forward Round 1: 333 peptides, 41 chains. Longest chain 23 peptides. Score 0.495 Round 2: 338 peptides, 38 chains. Longest chain 23 peptides. Score 0.524 Round 3: 331 peptides, 27 chains. Longest chain 51 peptides. Score 0.590 Round 4: 323 peptides, 35 chains. Longest chain 30 peptides. Score 0.523 Round 5: 329 peptides, 33 chains. Longest chain 32 peptides. Score 0.546 Taking the results from Round 3 Chains 31, Residues 304, Estimated correctness of the model 10.7 % 2 chains (56 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7498 restraints for refining 3742 atoms. 6087 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2693 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 12: After refmac, R = 0.2511 (Rfree = 0.000) for 3699 atoms. Found 22 (24 requested) and removed 15 (12 requested) atoms. Cycle 13: After refmac, R = 0.2398 (Rfree = 0.000) for 3679 atoms. Found 15 (23 requested) and removed 15 (11 requested) atoms. Cycle 14: After refmac, R = 0.2334 (Rfree = 0.000) for 3661 atoms. Found 16 (23 requested) and removed 16 (11 requested) atoms. Cycle 15: After refmac, R = 0.2277 (Rfree = 0.000) for 3650 atoms. Found 11 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 3805 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 3847 seeds are put forward Round 1: 336 peptides, 44 chains. Longest chain 21 peptides. Score 0.478 Round 2: 348 peptides, 35 chains. Longest chain 22 peptides. Score 0.560 Round 3: 348 peptides, 39 chains. Longest chain 26 peptides. Score 0.532 Round 4: 329 peptides, 32 chains. Longest chain 21 peptides. Score 0.553 Round 5: 345 peptides, 36 chains. Longest chain 24 peptides. Score 0.548 Taking the results from Round 2 Chains 35, Residues 313, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7889 restraints for refining 3742 atoms. 6594 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2617 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.2433 (Rfree = 0.000) for 3717 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 18: After refmac, R = 0.2311 (Rfree = 0.000) for 3709 atoms. Found 14 (23 requested) and removed 19 (11 requested) atoms. Cycle 19: After refmac, R = 0.2241 (Rfree = 0.000) for 3690 atoms. Found 15 (23 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.2189 (Rfree = 0.000) for 3677 atoms. Found 14 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 2.59 Search for helices and strands: 0 residues in 0 chains, 3833 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 3853 seeds are put forward Round 1: 328 peptides, 39 chains. Longest chain 29 peptides. Score 0.502 Round 2: 350 peptides, 36 chains. Longest chain 24 peptides. Score 0.556 Round 3: 351 peptides, 37 chains. Longest chain 23 peptides. Score 0.550 Round 4: 340 peptides, 33 chains. Longest chain 35 peptides. Score 0.562 Round 5: 339 peptides, 40 chains. Longest chain 23 peptides. Score 0.512 Taking the results from Round 4 Chains 37, Residues 307, Estimated correctness of the model 0.0 % 6 chains (85 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7159 restraints for refining 3742 atoms. 5613 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2659 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 22: After refmac, R = 0.2496 (Rfree = 0.000) for 3718 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 23: After refmac, R = 0.2372 (Rfree = 0.000) for 3690 atoms. Found 12 (23 requested) and removed 18 (11 requested) atoms. Cycle 24: After refmac, R = 0.2329 (Rfree = 0.000) for 3665 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Cycle 25: After refmac, R = 0.2258 (Rfree = 0.000) for 3653 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 2.56 Search for helices and strands: 0 residues in 0 chains, 3813 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3841 seeds are put forward Round 1: 348 peptides, 44 chains. Longest chain 19 peptides. Score 0.497 Round 2: 339 peptides, 41 chains. Longest chain 18 peptides. Score 0.504 Round 3: 339 peptides, 40 chains. Longest chain 28 peptides. Score 0.512 Round 4: 336 peptides, 39 chains. Longest chain 23 peptides. Score 0.514 Round 5: 332 peptides, 39 chains. Longest chain 24 peptides. Score 0.508 Taking the results from Round 4 Chains 41, Residues 297, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 8207 restraints for refining 3742 atoms. 7015 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2499 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 27: After refmac, R = 0.2346 (Rfree = 0.000) for 3716 atoms. Found 21 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.2250 (Rfree = 0.000) for 3707 atoms. Found 15 (23 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.2208 (Rfree = 0.000) for 3702 atoms. Found 10 (23 requested) and removed 19 (11 requested) atoms. Cycle 30: After refmac, R = 0.2237 (Rfree = 0.000) for 3677 atoms. Found 11 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 2.55 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3892 seeds are put forward Round 1: 327 peptides, 44 chains. Longest chain 26 peptides. Score 0.464 Round 2: 347 peptides, 44 chains. Longest chain 16 peptides. Score 0.495 Round 3: 339 peptides, 41 chains. Longest chain 20 peptides. Score 0.504 Round 4: 325 peptides, 35 chains. Longest chain 24 peptides. Score 0.526 Round 5: 333 peptides, 37 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 4 Chains 38, Residues 290, Estimated correctness of the model 0.0 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7851 restraints for refining 3742 atoms. 6514 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2630 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 32: After refmac, R = 0.2372 (Rfree = 0.000) for 3706 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 33: After refmac, R = 0.2270 (Rfree = 0.000) for 3688 atoms. Found 20 (23 requested) and removed 24 (11 requested) atoms. Cycle 34: After refmac, R = 0.2233 (Rfree = 0.000) for 3674 atoms. Found 13 (23 requested) and removed 19 (11 requested) atoms. Cycle 35: After refmac, R = 0.2217 (Rfree = 0.000) for 3650 atoms. Found 14 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 3797 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3820 seeds are put forward Round 1: 315 peptides, 43 chains. Longest chain 16 peptides. Score 0.451 Round 2: 339 peptides, 37 chains. Longest chain 21 peptides. Score 0.533 Round 3: 346 peptides, 36 chains. Longest chain 27 peptides. Score 0.550 Round 4: 337 peptides, 38 chains. Longest chain 21 peptides. Score 0.523 Round 5: 329 peptides, 34 chains. Longest chain 28 peptides. Score 0.539 Taking the results from Round 3 Chains 40, Residues 310, Estimated correctness of the model 0.0 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7527 restraints for refining 3742 atoms. 6112 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2519 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 37: After refmac, R = 0.2347 (Rfree = 0.000) for 3710 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 38: After refmac, R = 0.2263 (Rfree = 0.000) for 3705 atoms. Found 15 (23 requested) and removed 18 (11 requested) atoms. Cycle 39: After refmac, R = 0.2239 (Rfree = 0.000) for 3692 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 40: After refmac, R = 0.2198 (Rfree = 0.000) for 3692 atoms. Found 15 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3901 seeds are put forward Round 1: 317 peptides, 41 chains. Longest chain 26 peptides. Score 0.470 Round 2: 332 peptides, 38 chains. Longest chain 20 peptides. Score 0.515 Round 3: 323 peptides, 29 chains. Longest chain 26 peptides. Score 0.566 Round 4: 330 peptides, 38 chains. Longest chain 22 peptides. Score 0.512 Round 5: 342 peptides, 34 chains. Longest chain 29 peptides. Score 0.558 Taking the results from Round 3 Chains 31, Residues 294, Estimated correctness of the model 0.9 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7603 restraints for refining 3741 atoms. 6232 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2441 (Rfree = 0.000) for 3741 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 42: After refmac, R = 0.2297 (Rfree = 0.000) for 3713 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 43: After refmac, R = 0.2191 (Rfree = 0.000) for 3708 atoms. Found 17 (23 requested) and removed 19 (11 requested) atoms. Cycle 44: After refmac, R = 0.2138 (Rfree = 0.000) for 3697 atoms. Found 14 (23 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.2086 (Rfree = 0.000) for 3692 atoms. Found 12 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3913 seeds are put forward Round 1: 290 peptides, 42 chains. Longest chain 21 peptides. Score 0.417 Round 2: 324 peptides, 37 chains. Longest chain 22 peptides. Score 0.510 Round 3: 324 peptides, 34 chains. Longest chain 28 peptides. Score 0.532 Round 4: 321 peptides, 34 chains. Longest chain 21 peptides. Score 0.527 Round 5: 325 peptides, 31 chains. Longest chain 28 peptides. Score 0.554 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 294, Estimated correctness of the model 0.0 % 5 chains (57 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (294 residues) following loop building 5 chains (57 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11808 reflections ( 99.75 % complete ) and 7679 restraints for refining 3741 atoms. 6325 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2480 (Rfree = 0.000) for 3741 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2306 (Rfree = 0.000) for 3684 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2253 (Rfree = 0.000) for 3651 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2232 (Rfree = 0.000) for 3621 atoms. TimeTaking 298.78