Mon 24 Dec 07:30:24 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 1vp4-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-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/1vp4-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-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 07:30:29 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/1vp4-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-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 716 and 0 Target number of residues in the AU: 716 Target solvent content: 0.6401 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.2-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 3.200 Wilson plot Bfac: 72.01 Failed to save intermediate PDB 17764 reflections ( 99.82 % complete ) and 0 restraints for refining 7543 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3683 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3544 (Rfree = 0.000) for 7543 atoms. Found 67 (67 requested) and removed 148 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 7637 seeds are put forward NCS extension: 0 residues added, 7637 seeds are put forward Round 1: 342 peptides, 69 chains. Longest chain 10 peptides. Score 0.286 Round 2: 421 peptides, 72 chains. Longest chain 18 peptides. Score 0.392 Round 3: 461 peptides, 77 chains. Longest chain 16 peptides. Score 0.420 Round 4: 439 peptides, 68 chains. Longest chain 16 peptides. Score 0.445 Round 5: 462 peptides, 71 chains. Longest chain 20 peptides. Score 0.458 Taking the results from Round 5 Chains 72, Residues 391, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13443 restraints for refining 6207 atoms. 11803 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3001 (Rfree = 0.000) for 6207 atoms. Found 42 (55 requested) and removed 108 (27 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2937 (Rfree = 0.000) for 6104 atoms. Found 34 (55 requested) and removed 46 (27 requested) atoms. Cycle 3: After refmac, R = 0.2814 (Rfree = 0.000) for 6076 atoms. Found 20 (54 requested) and removed 42 (27 requested) atoms. Cycle 4: After refmac, R = 0.2871 (Rfree = 0.000) for 6040 atoms. Found 32 (54 requested) and removed 40 (27 requested) atoms. Cycle 5: After refmac, R = 0.3194 (Rfree = 0.000) for 6008 atoms. Found 54 (54 requested) and removed 69 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 6232 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6257 seeds are put forward Round 1: 425 peptides, 79 chains. Longest chain 11 peptides. Score 0.352 Round 2: 469 peptides, 74 chains. Longest chain 20 peptides. Score 0.450 Round 3: 512 peptides, 75 chains. Longest chain 16 peptides. Score 0.502 Round 4: 475 peptides, 72 chains. Longest chain 19 peptides. Score 0.470 Round 5: 469 peptides, 65 chains. Longest chain 24 peptides. Score 0.504 Taking the results from Round 5 Chains 66, Residues 404, Estimated correctness of the model 12.6 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13832 restraints for refining 6208 atoms. 12213 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2876 (Rfree = 0.000) for 6208 atoms. Found 35 (55 requested) and removed 54 (27 requested) atoms. Cycle 7: After refmac, R = 0.2805 (Rfree = 0.000) for 6158 atoms. Found 26 (55 requested) and removed 44 (27 requested) atoms. Cycle 8: After refmac, R = 0.2747 (Rfree = 0.000) for 6127 atoms. Found 25 (55 requested) and removed 34 (27 requested) atoms. Cycle 9: After refmac, R = 0.2606 (Rfree = 0.000) for 6101 atoms. Found 16 (54 requested) and removed 29 (27 requested) atoms. Cycle 10: After refmac, R = 0.2581 (Rfree = 0.000) for 6077 atoms. Found 25 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 6334 seeds are put forward NCS extension: 48 residues added (2 deleted due to clashes), 6382 seeds are put forward Round 1: 443 peptides, 80 chains. Longest chain 14 peptides. Score 0.374 Round 2: 502 peptides, 78 chains. Longest chain 24 peptides. Score 0.471 Round 3: 470 peptides, 62 chains. Longest chain 24 peptides. Score 0.523 Round 4: 482 peptides, 67 chains. Longest chain 18 peptides. Score 0.510 Round 5: 478 peptides, 66 chains. Longest chain 17 peptides. Score 0.510 Taking the results from Round 3 Chains 62, Residues 408, Estimated correctness of the model 18.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13944 restraints for refining 6207 atoms. 12374 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2628 (Rfree = 0.000) for 6207 atoms. Found 39 (55 requested) and removed 30 (27 requested) atoms. Cycle 12: After refmac, R = 0.2571 (Rfree = 0.000) for 6194 atoms. Found 28 (55 requested) and removed 35 (27 requested) atoms. Cycle 13: After refmac, R = 0.2452 (Rfree = 0.000) for 6173 atoms. Found 11 (55 requested) and removed 32 (27 requested) atoms. Cycle 14: After refmac, R = 0.2792 (Rfree = 0.000) for 6132 atoms. Found 54 (55 requested) and removed 32 (27 requested) atoms. Cycle 15: After refmac, R = 0.2340 (Rfree = 0.000) for 6137 atoms. Found 18 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 6352 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 6389 seeds are put forward Round 1: 453 peptides, 83 chains. Longest chain 14 peptides. Score 0.369 Round 2: 473 peptides, 75 chains. Longest chain 19 peptides. Score 0.449 Round 3: 468 peptides, 70 chains. Longest chain 16 peptides. Score 0.473 Round 4: 443 peptides, 65 chains. Longest chain 19 peptides. Score 0.469 Round 5: 459 peptides, 64 chains. Longest chain 14 peptides. Score 0.497 Taking the results from Round 5 Chains 66, Residues 395, Estimated correctness of the model 10.4 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13785 restraints for refining 6207 atoms. 12156 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2536 (Rfree = 0.000) for 6207 atoms. Found 25 (55 requested) and removed 40 (27 requested) atoms. Cycle 17: After refmac, R = 0.2421 (Rfree = 0.000) for 6173 atoms. Found 21 (55 requested) and removed 31 (27 requested) atoms. Cycle 18: After refmac, R = 0.2354 (Rfree = 0.000) for 6150 atoms. Found 16 (55 requested) and removed 28 (27 requested) atoms. Cycle 19: After refmac, R = 0.2581 (Rfree = 0.000) for 6124 atoms. Found 50 (55 requested) and removed 29 (27 requested) atoms. Cycle 20: After refmac, R = 0.2365 (Rfree = 0.000) for 6131 atoms. Found 20 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6364 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6379 seeds are put forward Round 1: 428 peptides, 70 chains. Longest chain 15 peptides. Score 0.416 Round 2: 452 peptides, 70 chains. Longest chain 17 peptides. Score 0.451 Round 3: 465 peptides, 69 chains. Longest chain 17 peptides. Score 0.475 Round 4: 459 peptides, 63 chains. Longest chain 27 peptides. Score 0.503 Round 5: 458 peptides, 60 chains. Longest chain 20 peptides. Score 0.519 Taking the results from Round 5 Chains 62, Residues 398, Estimated correctness of the model 17.4 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13630 restraints for refining 6207 atoms. 11996 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2538 (Rfree = 0.000) for 6207 atoms. Found 41 (55 requested) and removed 34 (27 requested) atoms. Cycle 22: After refmac, R = 0.2554 (Rfree = 0.000) for 6201 atoms. Found 36 (55 requested) and removed 32 (27 requested) atoms. Cycle 23: After refmac, R = 0.2779 (Rfree = 0.000) for 6190 atoms. Found 55 (55 requested) and removed 29 (27 requested) atoms. Cycle 24: After refmac, R = 0.2417 (Rfree = 0.000) for 6188 atoms. Found 33 (55 requested) and removed 34 (27 requested) atoms. Cycle 25: After refmac, R = 0.2443 (Rfree = 0.000) for 6177 atoms. Found 48 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 6411 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6432 seeds are put forward Round 1: 408 peptides, 73 chains. Longest chain 11 peptides. Score 0.366 Round 2: 449 peptides, 70 chains. Longest chain 15 peptides. Score 0.446 Round 3: 456 peptides, 67 chains. Longest chain 19 peptides. Score 0.475 Round 4: 453 peptides, 63 chains. Longest chain 16 peptides. Score 0.495 Round 5: 469 peptides, 65 chains. Longest chain 29 peptides. Score 0.504 Taking the results from Round 5 Chains 66, Residues 404, Estimated correctness of the model 12.6 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13541 restraints for refining 6208 atoms. 11875 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2565 (Rfree = 0.000) for 6208 atoms. Found 31 (55 requested) and removed 39 (27 requested) atoms. Cycle 27: After refmac, R = 0.2976 (Rfree = 0.000) for 6184 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Cycle 28: After refmac, R = 0.2768 (Rfree = 0.000) for 6172 atoms. Found 55 (55 requested) and removed 37 (27 requested) atoms. Cycle 29: After refmac, R = 0.2416 (Rfree = 0.000) for 6179 atoms. Found 30 (55 requested) and removed 32 (27 requested) atoms. Cycle 30: After refmac, R = 0.2706 (Rfree = 0.000) for 6165 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 6412 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 6439 seeds are put forward Round 1: 399 peptides, 73 chains. Longest chain 12 peptides. Score 0.352 Round 2: 423 peptides, 66 chains. Longest chain 15 peptides. Score 0.434 Round 3: 443 peptides, 65 chains. Longest chain 19 peptides. Score 0.469 Round 4: 450 peptides, 62 chains. Longest chain 32 peptides. Score 0.497 Round 5: 448 peptides, 65 chains. Longest chain 19 peptides. Score 0.476 Taking the results from Round 4 Chains 62, Residues 388, Estimated correctness of the model 10.4 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13182 restraints for refining 6207 atoms. 11526 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2618 (Rfree = 0.000) for 6207 atoms. Found 44 (55 requested) and removed 42 (27 requested) atoms. Cycle 32: After refmac, R = 0.2518 (Rfree = 0.000) for 6200 atoms. Found 22 (55 requested) and removed 36 (27 requested) atoms. Cycle 33: After refmac, R = 0.2496 (Rfree = 0.000) for 6179 atoms. Found 29 (55 requested) and removed 33 (27 requested) atoms. Cycle 34: After refmac, R = 0.2752 (Rfree = 0.000) for 6163 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 35: After refmac, R = 0.2477 (Rfree = 0.000) for 6170 atoms. Found 30 (55 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6386 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 6421 seeds are put forward Round 1: 370 peptides, 67 chains. Longest chain 21 peptides. Score 0.347 Round 2: 415 peptides, 61 chains. Longest chain 23 peptides. Score 0.455 Round 3: 441 peptides, 63 chains. Longest chain 19 peptides. Score 0.478 Round 4: 428 peptides, 65 chains. Longest chain 12 peptides. Score 0.448 Round 5: 418 peptides, 61 chains. Longest chain 22 peptides. Score 0.459 Taking the results from Round 3 Chains 64, Residues 378, Estimated correctness of the model 4.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13928 restraints for refining 6206 atoms. 12458 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2508 (Rfree = 0.000) for 6206 atoms. Found 29 (55 requested) and removed 33 (27 requested) atoms. Cycle 37: After refmac, R = 0.2783 (Rfree = 0.000) for 6190 atoms. Found 55 (55 requested) and removed 31 (27 requested) atoms. Cycle 38: After refmac, R = 0.2403 (Rfree = 0.000) for 6199 atoms. Found 32 (55 requested) and removed 34 (27 requested) atoms. Cycle 39: After refmac, R = 0.2310 (Rfree = 0.000) for 6175 atoms. Found 35 (55 requested) and removed 32 (27 requested) atoms. Cycle 40: After refmac, R = 0.2324 (Rfree = 0.000) for 6170 atoms. Found 36 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.00 Search for helices and strands: 0 residues in 0 chains, 6414 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6435 seeds are put forward Round 1: 311 peptides, 58 chains. Longest chain 13 peptides. Score 0.313 Round 2: 358 peptides, 55 chains. Longest chain 17 peptides. Score 0.410 Round 3: 375 peptides, 57 chains. Longest chain 17 peptides. Score 0.422 Round 4: 375 peptides, 55 chains. Longest chain 18 peptides. Score 0.436 Round 5: 379 peptides, 54 chains. Longest chain 27 peptides. Score 0.448 Taking the results from Round 5 Chains 55, Residues 325, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13882 restraints for refining 6208 atoms. 12561 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2468 (Rfree = 0.000) for 6208 atoms. Found 51 (55 requested) and removed 30 (27 requested) atoms. Cycle 42: After refmac, R = 0.2359 (Rfree = 0.000) for 6220 atoms. Found 27 (55 requested) and removed 28 (27 requested) atoms. Cycle 43: After refmac, R = 0.2293 (Rfree = 0.000) for 6205 atoms. Found 28 (55 requested) and removed 29 (27 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2765 (Rfree = 0.000) for 6194 atoms. Found 55 (55 requested) and removed 33 (27 requested) atoms. Cycle 45: After refmac, R = 0.2275 (Rfree = 0.000) for 6200 atoms. Found 23 (55 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 6406 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 6431 seeds are put forward Round 1: 299 peptides, 59 chains. Longest chain 14 peptides. Score 0.285 Round 2: 367 peptides, 69 chains. Longest chain 10 peptides. Score 0.328 Round 3: 364 peptides, 62 chains. Longest chain 13 peptides. Score 0.372 Round 4: 373 peptides, 63 chains. Longest chain 29 peptides. Score 0.379 Round 5: 384 peptides, 58 chains. Longest chain 17 peptides. Score 0.429 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 326, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 58 chains (326 residues) following loop building 5 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17764 reflections ( 99.82 % complete ) and 14045 restraints for refining 6208 atoms. 12747 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2382 (Rfree = 0.000) for 6208 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2813 (Rfree = 0.000) for 6170 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2385 (Rfree = 0.000) for 6121 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2193 (Rfree = 0.000) for 6082 atoms. TimeTaking 74.4