null Sun 23 Dec 22:23:08 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 2a2m-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-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/2a2m-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-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 22:23:18 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/2a2m-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-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 595 and 0 Target number of residues in the AU: 595 Target solvent content: 0.6601 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-3.8-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-3.8-parrot-hancs.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 3.801 Wilson plot Bfac: 84.92 10076 reflections ( 99.70 % complete ) and 0 restraints for refining 4593 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3414 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3332 (Rfree = 0.000) for 4593 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 2.73 Search for helices and strands: 0 residues in 0 chains, 4713 seeds are put forward NCS extension: 0 residues added, 4713 seeds are put forward Round 1: 290 peptides, 41 chains. Longest chain 20 peptides. Score 0.425 Round 2: 319 peptides, 34 chains. Longest chain 22 peptides. Score 0.524 Round 3: 320 peptides, 29 chains. Longest chain 23 peptides. Score 0.561 Round 4: 327 peptides, 31 chains. Longest chain 31 peptides. Score 0.557 Round 5: 327 peptides, 30 chains. Longest chain 25 peptides. Score 0.564 Taking the results from Round 5 Chains 34, Residues 297, Estimated correctness of the model 0.0 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7634 restraints for refining 3731 atoms. 6268 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2749 (Rfree = 0.000) for 3731 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 2: After refmac, R = 0.2654 (Rfree = 0.000) for 3630 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 3: After refmac, R = 0.2571 (Rfree = 0.000) for 3577 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 4: After refmac, R = 0.2395 (Rfree = 0.000) for 3552 atoms. Found 14 (19 requested) and removed 20 (9 requested) atoms. Cycle 5: After refmac, R = 0.2353 (Rfree = 0.000) for 3532 atoms. Found 14 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3704 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3727 seeds are put forward Round 1: 313 peptides, 36 chains. Longest chain 22 peptides. Score 0.501 Round 2: 324 peptides, 31 chains. Longest chain 23 peptides. Score 0.553 Round 3: 317 peptides, 34 chains. Longest chain 26 peptides. Score 0.521 Round 4: 319 peptides, 29 chains. Longest chain 41 peptides. Score 0.560 Round 5: 301 peptides, 29 chains. Longest chain 27 peptides. Score 0.534 Taking the results from Round 4 Chains 32, Residues 290, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7798 restraints for refining 3734 atoms. 6539 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2600 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 7: After refmac, R = 0.2693 (Rfree = 0.000) for 3694 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 8: After refmac, R = 0.2585 (Rfree = 0.000) for 3674 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 9: After refmac, R = 0.2501 (Rfree = 0.000) for 3662 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 10: After refmac, R = 0.2452 (Rfree = 0.000) for 3645 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 2.70 Search for helices and strands: 0 residues in 0 chains, 3852 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 3887 seeds are put forward Round 1: 310 peptides, 40 chains. Longest chain 24 peptides. Score 0.466 Round 2: 314 peptides, 31 chains. Longest chain 21 peptides. Score 0.538 Round 3: 302 peptides, 31 chains. Longest chain 21 peptides. Score 0.521 Round 4: 316 peptides, 30 chains. Longest chain 25 peptides. Score 0.549 Round 5: 311 peptides, 25 chains. Longest chain 27 peptides. Score 0.577 Taking the results from Round 5 Chains 28, Residues 286, Estimated correctness of the model 0.0 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7653 restraints for refining 3734 atoms. 6282 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2744 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 12: After refmac, R = 0.2549 (Rfree = 0.000) for 3680 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 13: After refmac, R = 0.2527 (Rfree = 0.000) for 3639 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 14: After refmac, R = 0.2526 (Rfree = 0.000) for 3622 atoms. Found 14 (20 requested) and removed 16 (10 requested) atoms. Cycle 15: After refmac, R = 0.2475 (Rfree = 0.000) for 3596 atoms. Found 14 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 2.71 Search for helices and strands: 0 residues in 0 chains, 3778 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3805 seeds are put forward Round 1: 298 peptides, 32 chains. Longest chain 27 peptides. Score 0.507 Round 2: 306 peptides, 31 chains. Longest chain 22 peptides. Score 0.527 Round 3: 281 peptides, 29 chains. Longest chain 23 peptides. Score 0.503 Round 4: 305 peptides, 29 chains. Longest chain 24 peptides. Score 0.540 Round 5: 309 peptides, 28 chains. Longest chain 29 peptides. Score 0.553 Taking the results from Round 5 Chains 30, Residues 281, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7735 restraints for refining 3733 atoms. 6464 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2798 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 17: After refmac, R = 0.2744 (Rfree = 0.000) for 3667 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 18: After refmac, R = 0.2607 (Rfree = 0.000) for 3624 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 19: After refmac, R = 0.2656 (Rfree = 0.000) for 3614 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 20: After refmac, R = 0.2600 (Rfree = 0.000) for 3603 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 49 residues added (1 deleted due to clashes), 3836 seeds are put forward Round 1: 291 peptides, 36 chains. Longest chain 24 peptides. Score 0.465 Round 2: 310 peptides, 31 chains. Longest chain 32 peptides. Score 0.533 Round 3: 307 peptides, 33 chains. Longest chain 28 peptides. Score 0.513 Round 4: 305 peptides, 32 chains. Longest chain 27 peptides. Score 0.518 Round 5: 308 peptides, 36 chains. Longest chain 28 peptides. Score 0.493 Taking the results from Round 2 Chains 33, Residues 279, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 8004 restraints for refining 3733 atoms. 6839 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2698 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 22: After refmac, R = 0.2646 (Rfree = 0.000) for 3670 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 23: After refmac, R = 0.2633 (Rfree = 0.000) for 3631 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 24: After refmac, R = 0.2634 (Rfree = 0.000) for 3601 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 25: After refmac, R = 0.2591 (Rfree = 0.000) for 3569 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3738 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3767 seeds are put forward Round 1: 293 peptides, 43 chains. Longest chain 15 peptides. Score 0.414 Round 2: 317 peptides, 35 chains. Longest chain 25 peptides. Score 0.514 Round 3: 311 peptides, 35 chains. Longest chain 34 peptides. Score 0.505 Round 4: 304 peptides, 32 chains. Longest chain 22 peptides. Score 0.516 Round 5: 299 peptides, 32 chains. Longest chain 24 peptides. Score 0.509 Taking the results from Round 4 Chains 33, Residues 272, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 8136 restraints for refining 3733 atoms. 7004 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2767 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 27: After refmac, R = 0.2577 (Rfree = 0.000) for 3683 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 28: After refmac, R = 0.2520 (Rfree = 0.000) for 3652 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 29: After refmac, R = 0.2429 (Rfree = 0.000) for 3646 atoms. Found 18 (20 requested) and removed 20 (10 requested) atoms. Cycle 30: After refmac, R = 0.2380 (Rfree = 0.000) for 3630 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 2.74 Search for helices and strands: 0 residues in 0 chains, 3801 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3822 seeds are put forward Round 1: 283 peptides, 42 chains. Longest chain 12 peptides. Score 0.405 Round 2: 307 peptides, 34 chains. Longest chain 21 peptides. Score 0.506 Round 3: 298 peptides, 31 chains. Longest chain 19 peptides. Score 0.514 Round 4: 293 peptides, 32 chains. Longest chain 20 peptides. Score 0.499 Round 5: 295 peptides, 27 chains. Longest chain 30 peptides. Score 0.539 Taking the results from Round 5 Chains 27, Residues 268, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7823 restraints for refining 3734 atoms. 6651 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2700 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 32: After refmac, R = 0.2596 (Rfree = 0.000) for 3683 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 33: After refmac, R = 0.2501 (Rfree = 0.000) for 3655 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 34: After refmac, R = 0.2458 (Rfree = 0.000) for 3637 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 35: After refmac, R = 0.2399 (Rfree = 0.000) for 3628 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 2.73 Search for helices and strands: 0 residues in 0 chains, 3801 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3830 seeds are put forward Round 1: 278 peptides, 38 chains. Longest chain 20 peptides. Score 0.428 Round 2: 301 peptides, 31 chains. Longest chain 22 peptides. Score 0.519 Round 3: 313 peptides, 33 chains. Longest chain 19 peptides. Score 0.522 Round 4: 296 peptides, 31 chains. Longest chain 27 peptides. Score 0.511 Round 5: 306 peptides, 33 chains. Longest chain 41 peptides. Score 0.512 Taking the results from Round 3 Chains 36, Residues 280, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 8014 restraints for refining 3733 atoms. 6839 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2627 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 37: After refmac, R = 0.2548 (Rfree = 0.000) for 3692 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 38: After refmac, R = 0.2512 (Rfree = 0.000) for 3670 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.2459 (Rfree = 0.000) for 3651 atoms. Found 19 (20 requested) and removed 16 (10 requested) atoms. Cycle 40: After refmac, R = 0.2493 (Rfree = 0.000) for 3639 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 2.72 Search for helices and strands: 0 residues in 0 chains, 3831 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3854 seeds are put forward Round 1: 268 peptides, 40 chains. Longest chain 16 peptides. Score 0.394 Round 2: 286 peptides, 29 chains. Longest chain 23 peptides. Score 0.511 Round 3: 271 peptides, 33 chains. Longest chain 17 peptides. Score 0.456 Round 4: 271 peptides, 33 chains. Longest chain 18 peptides. Score 0.456 Round 5: 290 peptides, 29 chains. Longest chain 30 peptides. Score 0.517 Taking the results from Round 5 Chains 29, Residues 261, Estimated correctness of the model 0.0 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7785 restraints for refining 3734 atoms. 6618 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2614 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 42: After refmac, R = 0.2474 (Rfree = 0.000) for 3691 atoms. Found 15 (20 requested) and removed 20 (10 requested) atoms. Cycle 43: After refmac, R = 0.2515 (Rfree = 0.000) for 3651 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 44: After refmac, R = 0.2362 (Rfree = 0.000) for 3634 atoms. Found 7 (20 requested) and removed 20 (10 requested) atoms. Cycle 45: After refmac, R = 0.2346 (Rfree = 0.000) for 3593 atoms. Found 16 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3790 seeds are put forward NCS extension: 41 residues added (3 deleted due to clashes), 3831 seeds are put forward Round 1: 265 peptides, 43 chains. Longest chain 13 peptides. Score 0.364 Round 2: 284 peptides, 32 chains. Longest chain 19 peptides. Score 0.485 Round 3: 281 peptides, 31 chains. Longest chain 16 peptides. Score 0.488 Round 4: 286 peptides, 33 chains. Longest chain 22 peptides. Score 0.480 Round 5: 282 peptides, 32 chains. Longest chain 23 peptides. Score 0.482 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 250, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (250 residues) following loop building 3 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10076 reflections ( 99.70 % complete ) and 7933 restraints for refining 3692 atoms. 6895 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2505 (Rfree = 0.000) for 3692 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2484 (Rfree = 0.000) for 3649 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2521 (Rfree = 0.000) for 3600 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2557 (Rfree = 0.000) for 3570 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:27:20 GMT 2018 Job finished. TimeTaking 244.2 Used memory is bytes: 17784464