Mon 24 Dec 00:36:31 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 2fno-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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/2fno-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 00:36:36 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/2fno-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 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-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.2-parrot-mrncs.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 4432 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3139 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2972 (Rfree = 0.000) for 4432 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 4521 seeds are put forward NCS extension: 0 residues added, 4521 seeds are put forward Round 1: 237 peptides, 43 chains. Longest chain 11 peptides. Score 0.368 Round 2: 281 peptides, 40 chains. Longest chain 17 peptides. Score 0.516 Round 3: 302 peptides, 44 chains. Longest chain 16 peptides. Score 0.524 Round 4: 307 peptides, 39 chains. Longest chain 19 peptides. Score 0.584 Round 5: 302 peptides, 40 chains. Longest chain 20 peptides. Score 0.564 Taking the results from Round 4 Chains 39, Residues 268, Estimated correctness of the model 36.7 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7726 restraints for refining 3621 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2745 (Rfree = 0.000) for 3621 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 2: After refmac, R = 0.2637 (Rfree = 0.000) for 3574 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 3: After refmac, R = 0.2580 (Rfree = 0.000) for 3558 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 4: After refmac, R = 0.2439 (Rfree = 0.000) for 3544 atoms. Found 26 (31 requested) and removed 29 (15 requested) atoms. Cycle 5: After refmac, R = 0.2441 (Rfree = 0.000) for 3532 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 3681 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3710 seeds are put forward Round 1: 276 peptides, 42 chains. Longest chain 18 peptides. Score 0.483 Round 2: 318 peptides, 41 chains. Longest chain 23 peptides. Score 0.588 Round 3: 314 peptides, 45 chains. Longest chain 19 peptides. Score 0.541 Round 4: 306 peptides, 43 chains. Longest chain 15 peptides. Score 0.543 Round 5: 323 peptides, 41 chains. Longest chain 23 peptides. Score 0.598 Taking the results from Round 5 Chains 44, Residues 282, Estimated correctness of the model 40.5 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7682 restraints for refining 3623 atoms. 6480 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2667 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 7: After refmac, R = 0.2398 (Rfree = 0.000) for 3614 atoms. Found 24 (32 requested) and removed 25 (16 requested) atoms. Cycle 8: After refmac, R = 0.2436 (Rfree = 0.000) for 3601 atoms. Found 21 (32 requested) and removed 28 (16 requested) atoms. Cycle 9: After refmac, R = 0.2360 (Rfree = 0.000) for 3578 atoms. Found 29 (32 requested) and removed 22 (16 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2205 (Rfree = 0.000) for 3569 atoms. Found 23 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 3698 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 3710 seeds are put forward Round 1: 280 peptides, 48 chains. Longest chain 14 peptides. Score 0.427 Round 2: 299 peptides, 41 chains. Longest chain 16 peptides. Score 0.547 Round 3: 315 peptides, 41 chains. Longest chain 19 peptides. Score 0.582 Round 4: 310 peptides, 39 chains. Longest chain 23 peptides. Score 0.590 Round 5: 328 peptides, 46 chains. Longest chain 19 peptides. Score 0.562 Taking the results from Round 4 Chains 40, Residues 271, Estimated correctness of the model 38.3 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7825 restraints for refining 3622 atoms. 6672 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2576 (Rfree = 0.000) for 3622 atoms. Found 29 (32 requested) and removed 26 (16 requested) atoms. Cycle 12: After refmac, R = 0.2430 (Rfree = 0.000) for 3611 atoms. Found 22 (32 requested) and removed 22 (16 requested) atoms. Cycle 13: After refmac, R = 0.2365 (Rfree = 0.000) for 3604 atoms. Found 16 (32 requested) and removed 17 (16 requested) atoms. Cycle 14: After refmac, R = 0.2378 (Rfree = 0.000) for 3598 atoms. Found 21 (32 requested) and removed 19 (16 requested) atoms. Cycle 15: After refmac, R = 0.2300 (Rfree = 0.000) for 3596 atoms. Found 13 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 3742 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3762 seeds are put forward Round 1: 256 peptides, 40 chains. Longest chain 13 peptides. Score 0.454 Round 2: 302 peptides, 43 chains. Longest chain 18 peptides. Score 0.534 Round 3: 291 peptides, 39 chains. Longest chain 23 peptides. Score 0.549 Round 4: 298 peptides, 37 chains. Longest chain 26 peptides. Score 0.584 Round 5: 297 peptides, 37 chains. Longest chain 17 peptides. Score 0.582 Taking the results from Round 4 Chains 38, Residues 261, Estimated correctness of the model 36.7 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7944 restraints for refining 3623 atoms. 6897 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2408 (Rfree = 0.000) for 3623 atoms. Found 19 (32 requested) and removed 16 (16 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 3619 atoms. Found 21 (32 requested) and removed 21 (16 requested) atoms. Cycle 18: After refmac, R = 0.2186 (Rfree = 0.000) for 3606 atoms. Found 7 (32 requested) and removed 17 (16 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 3589 atoms. Found 12 (32 requested) and removed 17 (16 requested) atoms. Cycle 20: After refmac, R = 0.2004 (Rfree = 0.000) for 3584 atoms. Found 5 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3719 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3734 seeds are put forward Round 1: 251 peptides, 45 chains. Longest chain 13 peptides. Score 0.383 Round 2: 281 peptides, 42 chains. Longest chain 15 peptides. Score 0.495 Round 3: 277 peptides, 38 chains. Longest chain 15 peptides. Score 0.527 Round 4: 291 peptides, 41 chains. Longest chain 23 peptides. Score 0.529 Round 5: 285 peptides, 41 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 4 Chains 42, Residues 250, Estimated correctness of the model 20.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8109 restraints for refining 3623 atoms. 7118 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2249 (Rfree = 0.000) for 3623 atoms. Found 30 (32 requested) and removed 18 (16 requested) atoms. Cycle 22: After refmac, R = 0.2296 (Rfree = 0.000) for 3624 atoms. Found 21 (32 requested) and removed 18 (16 requested) atoms. Cycle 23: After refmac, R = 0.2153 (Rfree = 0.000) for 3621 atoms. Found 11 (32 requested) and removed 16 (16 requested) atoms. Cycle 24: After refmac, R = 0.2150 (Rfree = 0.000) for 3611 atoms. Found 15 (32 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.2122 (Rfree = 0.000) for 3602 atoms. Found 20 (32 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, 3742 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3762 seeds are put forward Round 1: 251 peptides, 47 chains. Longest chain 11 peptides. Score 0.360 Round 2: 271 peptides, 40 chains. Longest chain 13 peptides. Score 0.492 Round 3: 283 peptides, 44 chains. Longest chain 13 peptides. Score 0.478 Round 4: 281 peptides, 43 chains. Longest chain 13 peptides. Score 0.484 Round 5: 275 peptides, 40 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 41, Residues 235, Estimated correctness of the model 12.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8095 restraints for refining 3623 atoms. 7119 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2364 (Rfree = 0.000) for 3623 atoms. Found 31 (32 requested) and removed 19 (16 requested) atoms. Cycle 27: After refmac, R = 0.2140 (Rfree = 0.000) for 3621 atoms. Found 23 (32 requested) and removed 17 (16 requested) atoms. Cycle 28: After refmac, R = 0.2134 (Rfree = 0.000) for 3616 atoms. Found 16 (32 requested) and removed 16 (16 requested) atoms. Cycle 29: After refmac, R = 0.2129 (Rfree = 0.000) for 3609 atoms. Found 17 (32 requested) and removed 17 (16 requested) atoms. Cycle 30: After refmac, R = 0.2160 (Rfree = 0.000) for 3607 atoms. Found 17 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 3747 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 3780 seeds are put forward Round 1: 253 peptides, 47 chains. Longest chain 11 peptides. Score 0.365 Round 2: 284 peptides, 40 chains. Longest chain 15 peptides. Score 0.523 Round 3: 287 peptides, 41 chains. Longest chain 16 peptides. Score 0.520 Round 4: 277 peptides, 35 chains. Longest chain 23 peptides. Score 0.558 Round 5: 292 peptides, 39 chains. Longest chain 19 peptides. Score 0.551 Taking the results from Round 4 Chains 35, Residues 242, Estimated correctness of the model 29.2 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8284 restraints for refining 3623 atoms. 7332 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2366 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 32: After refmac, R = 0.2215 (Rfree = 0.000) for 3627 atoms. Found 17 (32 requested) and removed 17 (16 requested) atoms. Cycle 33: After refmac, R = 0.2175 (Rfree = 0.000) for 3614 atoms. Found 18 (32 requested) and removed 16 (16 requested) atoms. Cycle 34: After refmac, R = 0.2098 (Rfree = 0.000) for 3611 atoms. Found 12 (32 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.2108 (Rfree = 0.000) for 3597 atoms. Found 7 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3747 seeds are put forward NCS extension: 42 residues added (3 deleted due to clashes), 3789 seeds are put forward Round 1: 208 peptides, 34 chains. Longest chain 13 peptides. Score 0.396 Round 2: 257 peptides, 37 chains. Longest chain 16 peptides. Score 0.490 Round 3: 254 peptides, 36 chains. Longest chain 14 peptides. Score 0.494 Round 4: 266 peptides, 35 chains. Longest chain 16 peptides. Score 0.533 Round 5: 261 peptides, 38 chains. Longest chain 16 peptides. Score 0.489 Taking the results from Round 4 Chains 35, Residues 231, Estimated correctness of the model 21.7 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8065 restraints for refining 3623 atoms. 7128 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2315 (Rfree = 0.000) for 3623 atoms. Found 26 (32 requested) and removed 18 (16 requested) atoms. Cycle 37: After refmac, R = 0.2196 (Rfree = 0.000) for 3623 atoms. Found 22 (32 requested) and removed 19 (16 requested) atoms. Cycle 38: After refmac, R = 0.2155 (Rfree = 0.000) for 3617 atoms. Found 16 (32 requested) and removed 16 (16 requested) atoms. Cycle 39: After refmac, R = 0.2066 (Rfree = 0.000) for 3610 atoms. Found 8 (32 requested) and removed 18 (16 requested) atoms. Cycle 40: After refmac, R = 0.2521 (Rfree = 0.000) for 3597 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3769 seeds are put forward Round 1: 215 peptides, 40 chains. Longest chain 13 peptides. Score 0.342 Round 2: 257 peptides, 42 chains. Longest chain 13 peptides. Score 0.434 Round 3: 260 peptides, 39 chains. Longest chain 24 peptides. Score 0.476 Round 4: 241 peptides, 37 chains. Longest chain 13 peptides. Score 0.450 Round 5: 243 peptides, 36 chains. Longest chain 20 peptides. Score 0.466 Taking the results from Round 3 Chains 39, Residues 221, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8442 restraints for refining 3623 atoms. 7597 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2239 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 42: After refmac, R = 0.2465 (Rfree = 0.000) for 3625 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 43: After refmac, R = 0.2159 (Rfree = 0.000) for 3630 atoms. Found 28 (32 requested) and removed 17 (16 requested) atoms. Cycle 44: After refmac, R = 0.2021 (Rfree = 0.000) for 3637 atoms. Found 19 (32 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.2082 (Rfree = 0.000) for 3636 atoms. Found 26 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3790 seeds are put forward NCS extension: 31 residues added (5 deleted due to clashes), 3821 seeds are put forward Round 1: 214 peptides, 39 chains. Longest chain 13 peptides. Score 0.351 Round 2: 248 peptides, 35 chains. Longest chain 23 peptides. Score 0.490 Round 3: 242 peptides, 40 chains. Longest chain 18 peptides. Score 0.418 Round 4: 236 peptides, 36 chains. Longest chain 15 peptides. Score 0.448 Round 5: 225 peptides, 36 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 213, Estimated correctness of the model 8.1 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 4 % 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 8285 restraints for refining 3623 atoms. 7433 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2158 (Rfree = 0.000) for 3623 atoms. Found 0 (32 requested) and removed 14 (16 requested) atoms. Cycle 47: After refmac, R = 0.2169 (Rfree = 0.000) for 3603 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2189 (Rfree = 0.000) for 3583 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2148 (Rfree = 0.000) for 3564 atoms. TimeTaking 51.28