null Mon 24 Dec 07:41:25 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 2fno-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.2-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/2fno-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.2-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 07:41:29 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/2fno-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.2-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 412 and 0 Target number of residues in the AU: 412 Target solvent content: 0.6203 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.2-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.75 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: 106.006 3.200 Wilson plot Bfac: 61.57 9774 reflections ( 99.42 % complete ) and 0 restraints for refining 4398 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3138 (Rfree = 0.000) for 4398 atoms. Found 39 (39 requested) and removed 47 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4514 seeds are put forward NCS extension: 0 residues added, 4514 seeds are put forward Round 1: 236 peptides, 45 chains. Longest chain 17 peptides. Score 0.341 Round 2: 281 peptides, 43 chains. Longest chain 17 peptides. Score 0.484 Round 3: 282 peptides, 44 chains. Longest chain 18 peptides. Score 0.476 Round 4: 311 peptides, 43 chains. Longest chain 17 peptides. Score 0.554 Round 5: 307 peptides, 43 chains. Longest chain 17 peptides. Score 0.545 Taking the results from Round 4 Chains 44, Residues 268, Estimated correctness of the model 28.1 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7757 restraints for refining 3623 atoms. 6615 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2700 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 2: After refmac, R = 0.2634 (Rfree = 0.000) for 3588 atoms. Found 28 (32 requested) and removed 24 (16 requested) atoms. Cycle 3: After refmac, R = 0.2559 (Rfree = 0.000) for 3579 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 4: After refmac, R = 0.2516 (Rfree = 0.000) for 3568 atoms. Found 24 (32 requested) and removed 21 (16 requested) atoms. Cycle 5: After refmac, R = 0.2577 (Rfree = 0.000) for 3558 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 3683 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3699 seeds are put forward Round 1: 275 peptides, 45 chains. Longest chain 16 peptides. Score 0.447 Round 2: 294 peptides, 42 chains. Longest chain 21 peptides. Score 0.526 Round 3: 289 peptides, 42 chains. Longest chain 16 peptides. Score 0.514 Round 4: 312 peptides, 41 chains. Longest chain 22 peptides. Score 0.575 Round 5: 315 peptides, 38 chains. Longest chain 21 peptides. Score 0.610 Taking the results from Round 5 Chains 42, Residues 277, Estimated correctness of the model 43.7 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7666 restraints for refining 3622 atoms. 6449 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 7: After refmac, R = 0.2472 (Rfree = 0.000) for 3607 atoms. Found 16 (32 requested) and removed 19 (16 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 3591 atoms. Found 19 (32 requested) and removed 19 (16 requested) atoms. Cycle 9: After refmac, R = 0.2233 (Rfree = 0.000) for 3582 atoms. Found 8 (32 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.2264 (Rfree = 0.000) for 3565 atoms. Found 19 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3699 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3724 seeds are put forward Round 1: 277 peptides, 42 chains. Longest chain 20 peptides. Score 0.485 Round 2: 307 peptides, 38 chains. Longest chain 22 peptides. Score 0.593 Round 3: 296 peptides, 40 chains. Longest chain 15 peptides. Score 0.550 Round 4: 297 peptides, 37 chains. Longest chain 21 peptides. Score 0.582 Round 5: 315 peptides, 34 chains. Longest chain 25 peptides. Score 0.645 Taking the results from Round 5 Chains 35, Residues 281, Estimated correctness of the model 52.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7836 restraints for refining 3623 atoms. 6705 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2611 (Rfree = 0.000) for 3623 atoms. Found 29 (32 requested) and removed 25 (16 requested) atoms. Cycle 12: After refmac, R = 0.2597 (Rfree = 0.000) for 3618 atoms. Found 28 (32 requested) and removed 19 (16 requested) atoms. Cycle 13: After refmac, R = 0.2476 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 14: After refmac, R = 0.2475 (Rfree = 0.000) for 3628 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. Cycle 15: After refmac, R = 0.2359 (Rfree = 0.000) for 3629 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3757 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3781 seeds are put forward Round 1: 280 peptides, 42 chains. Longest chain 16 peptides. Score 0.492 Round 2: 287 peptides, 39 chains. Longest chain 15 peptides. Score 0.540 Round 3: 303 peptides, 40 chains. Longest chain 15 peptides. Score 0.566 Round 4: 296 peptides, 35 chains. Longest chain 32 peptides. Score 0.599 Round 5: 284 peptides, 37 chains. Longest chain 19 peptides. Score 0.554 Taking the results from Round 4 Chains 36, Residues 261, Estimated correctness of the model 40.8 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7792 restraints for refining 3623 atoms. 6681 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2611 (Rfree = 0.000) for 3623 atoms. Found 26 (32 requested) and removed 19 (16 requested) atoms. Cycle 17: After refmac, R = 0.2505 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 18: After refmac, R = 0.2467 (Rfree = 0.000) for 3618 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 19: After refmac, R = 0.2557 (Rfree = 0.000) for 3627 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 20: After refmac, R = 0.2433 (Rfree = 0.000) for 3627 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3771 seeds are put forward Round 1: 268 peptides, 44 chains. Longest chain 16 peptides. Score 0.440 Round 2: 301 peptides, 38 chains. Longest chain 21 peptides. Score 0.581 Round 3: 311 peptides, 37 chains. Longest chain 23 peptides. Score 0.611 Round 4: 286 peptides, 38 chains. Longest chain 21 peptides. Score 0.548 Round 5: 293 peptides, 40 chains. Longest chain 26 peptides. Score 0.544 Taking the results from Round 3 Chains 41, Residues 274, Estimated correctness of the model 44.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7652 restraints for refining 3623 atoms. 6463 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3220 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 62 (16 requested) atoms. Cycle 22: After refmac, R = 0.2520 (Rfree = 0.000) for 3576 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 23: After refmac, R = 0.2360 (Rfree = 0.000) for 3573 atoms. Found 9 (32 requested) and removed 18 (16 requested) atoms. Cycle 24: After refmac, R = 0.2341 (Rfree = 0.000) for 3561 atoms. Found 9 (31 requested) and removed 17 (15 requested) atoms. Cycle 25: After refmac, R = 0.2349 (Rfree = 0.000) for 3549 atoms. Found 11 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 2.91 Search for helices and strands: 0 residues in 0 chains, 3689 seeds are put forward NCS extension: 42 residues added (3 deleted due to clashes), 3731 seeds are put forward Round 1: 260 peptides, 43 chains. Longest chain 14 peptides. Score 0.431 Round 2: 289 peptides, 37 chains. Longest chain 19 peptides. Score 0.565 Round 3: 299 peptides, 40 chains. Longest chain 23 peptides. Score 0.557 Round 4: 290 peptides, 35 chains. Longest chain 27 peptides. Score 0.586 Round 5: 291 peptides, 37 chains. Longest chain 24 peptides. Score 0.569 Taking the results from Round 4 Chains 35, Residues 255, Estimated correctness of the model 37.2 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7809 restraints for refining 3623 atoms. 6700 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2789 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 27: After refmac, R = 0.2798 (Rfree = 0.000) for 3602 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 28: After refmac, R = 0.2485 (Rfree = 0.000) for 3595 atoms. Found 25 (32 requested) and removed 16 (16 requested) atoms. Cycle 29: After refmac, R = 0.2422 (Rfree = 0.000) for 3593 atoms. Found 23 (32 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2231 (Rfree = 0.000) for 3590 atoms. Found 12 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3731 seeds are put forward Round 1: 218 peptides, 41 chains. Longest chain 11 peptides. Score 0.338 Round 2: 262 peptides, 41 chains. Longest chain 15 peptides. Score 0.459 Round 3: 277 peptides, 43 chains. Longest chain 21 peptides. Score 0.474 Round 4: 282 peptides, 38 chains. Longest chain 26 peptides. Score 0.539 Round 5: 272 peptides, 39 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 4 Chains 38, Residues 244, Estimated correctness of the model 23.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8075 restraints for refining 3622 atoms. 7137 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2649 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 32: After refmac, R = 0.2303 (Rfree = 0.000) for 3623 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. Cycle 33: After refmac, R = 0.2301 (Rfree = 0.000) for 3611 atoms. Found 21 (32 requested) and removed 18 (16 requested) atoms. Cycle 34: After refmac, R = 0.2164 (Rfree = 0.000) for 3605 atoms. Found 14 (32 requested) and removed 21 (16 requested) atoms. Cycle 35: After refmac, R = 0.2108 (Rfree = 0.000) for 3593 atoms. Found 3 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 3717 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 3757 seeds are put forward Round 1: 234 peptides, 41 chains. Longest chain 12 peptides. Score 0.384 Round 2: 252 peptides, 39 chains. Longest chain 20 peptides. Score 0.455 Round 3: 255 peptides, 38 chains. Longest chain 18 peptides. Score 0.474 Round 4: 242 peptides, 33 chains. Longest chain 15 peptides. Score 0.497 Round 5: 242 peptides, 35 chains. Longest chain 16 peptides. Score 0.475 Taking the results from Round 4 Chains 33, Residues 209, Estimated correctness of the model 10.4 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8301 restraints for refining 3623 atoms. 7483 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2660 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 37: After refmac, R = 0.2616 (Rfree = 0.000) for 3628 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.2404 (Rfree = 0.000) for 3625 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 39: After refmac, R = 0.2202 (Rfree = 0.000) for 3629 atoms. Found 20 (32 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.2249 (Rfree = 0.000) for 3627 atoms. Found 31 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 3743 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3763 seeds are put forward Round 1: 219 peptides, 39 chains. Longest chain 12 peptides. Score 0.366 Round 2: 239 peptides, 41 chains. Longest chain 12 peptides. Score 0.398 Round 3: 249 peptides, 37 chains. Longest chain 14 peptides. Score 0.470 Round 4: 242 peptides, 40 chains. Longest chain 16 peptides. Score 0.418 Round 5: 237 peptides, 41 chains. Longest chain 15 peptides. Score 0.392 Taking the results from Round 3 Chains 38, Residues 212, Estimated correctness of the model 1.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8149 restraints for refining 3623 atoms. 7318 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2428 (Rfree = 0.000) for 3623 atoms. Found 29 (32 requested) and removed 39 (16 requested) atoms. Cycle 42: After refmac, R = 0.2272 (Rfree = 0.000) for 3605 atoms. Found 28 (32 requested) and removed 18 (16 requested) atoms. Cycle 43: After refmac, R = 0.2300 (Rfree = 0.000) for 3609 atoms. Found 27 (32 requested) and removed 20 (16 requested) atoms. Cycle 44: After refmac, R = 0.2242 (Rfree = 0.000) for 3611 atoms. Found 18 (32 requested) and removed 17 (16 requested) atoms. Cycle 45: After refmac, R = 0.2165 (Rfree = 0.000) for 3605 atoms. Found 25 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3719 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3740 seeds are put forward Round 1: 204 peptides, 38 chains. Longest chain 11 peptides. Score 0.335 Round 2: 251 peptides, 40 chains. Longest chain 14 peptides. Score 0.441 Round 3: 264 peptides, 39 chains. Longest chain 18 peptides. Score 0.486 Round 4: 247 peptides, 42 chains. Longest chain 17 peptides. Score 0.408 Round 5: 259 peptides, 41 chains. Longest chain 16 peptides. Score 0.451 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 225, Estimated correctness of the model 6.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9774 reflections ( 99.42 % complete ) and 8140 restraints for refining 3621 atoms. 7279 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2786 (Rfree = 0.000) for 3621 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2412 (Rfree = 0.000) for 3595 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2362 (Rfree = 0.000) for 3573 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2335 (Rfree = 0.000) for 3552 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:25:06 GMT 2018 Job finished. TimeTaking 43.69 Used memory is bytes: 16487112