Sun 23 Dec 22:22:42 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 1vmi-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.2-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/1vmi-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.2-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 22:22:57 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/1vmi-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.2-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 302 and 0 Target number of residues in the AU: 302 Target solvent content: 0.6377 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.57 Input MTZ file: 1vmi-3.2-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: 182 Cell parameters: 94.674 94.674 174.359 90.000 90.000 120.000 Input sequence file: 1vmi-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.65 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.180 3.200 Wilson plot Bfac: 70.29 8159 reflections ( 99.74 % complete ) and 0 restraints for refining 3128 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3326 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3102 (Rfree = 0.000) for 3128 atoms. Found 23 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward Round 1: 166 peptides, 29 chains. Longest chain 12 peptides. Score 0.373 Round 2: 218 peptides, 29 chains. Longest chain 16 peptides. Score 0.545 Round 3: 223 peptides, 25 chains. Longest chain 20 peptides. Score 0.610 Round 4: 231 peptides, 26 chains. Longest chain 21 peptides. Score 0.619 Round 5: 219 peptides, 25 chains. Longest chain 22 peptides. Score 0.599 Taking the results from Round 4 Chains 29, Residues 205, Estimated correctness of the model 46.1 % 7 chains (75 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8159 reflections ( 99.74 % complete ) and 4815 restraints for refining 2535 atoms. 3766 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3152 (Rfree = 0.000) for 2535 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 2: After refmac, R = 0.2990 (Rfree = 0.000) for 2444 atoms. Found 22 (22 requested) and removed 47 (11 requested) atoms. Cycle 3: After refmac, R = 0.2992 (Rfree = 0.000) for 2386 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 4: After refmac, R = 0.2809 (Rfree = 0.000) for 2357 atoms. Found 10 (21 requested) and removed 17 (10 requested) atoms. Cycle 5: After refmac, R = 0.2727 (Rfree = 0.000) for 2339 atoms. Found 7 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2441 seeds are put forward Round 1: 213 peptides, 27 chains. Longest chain 25 peptides. Score 0.557 Round 2: 241 peptides, 26 chains. Longest chain 21 peptides. Score 0.644 Round 3: 238 peptides, 28 chains. Longest chain 36 peptides. Score 0.613 Round 4: 235 peptides, 25 chains. Longest chain 20 peptides. Score 0.640 Round 5: 233 peptides, 24 chains. Longest chain 24 peptides. Score 0.647 Taking the results from Round 5 Chains 26, Residues 209, Estimated correctness of the model 53.1 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 4959 restraints for refining 2492 atoms. 4030 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3138 (Rfree = 0.000) for 2492 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 7: After refmac, R = 0.2962 (Rfree = 0.000) for 2448 atoms. Found 14 (22 requested) and removed 22 (11 requested) atoms. Cycle 8: After refmac, R = 0.3069 (Rfree = 0.000) for 2418 atoms. Found 12 (21 requested) and removed 15 (10 requested) atoms. Cycle 9: After refmac, R = 0.2945 (Rfree = 0.000) for 2399 atoms. Found 14 (21 requested) and removed 16 (10 requested) atoms. Cycle 10: After refmac, R = 0.2773 (Rfree = 0.000) for 2386 atoms. Found 9 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 2476 seeds are put forward Round 1: 206 peptides, 26 chains. Longest chain 19 peptides. Score 0.550 Round 2: 219 peptides, 23 chains. Longest chain 23 peptides. Score 0.624 Round 3: 208 peptides, 24 chains. Longest chain 19 peptides. Score 0.582 Round 4: 220 peptides, 23 chains. Longest chain 39 peptides. Score 0.626 Round 5: 225 peptides, 24 chains. Longest chain 22 peptides. Score 0.627 Taking the results from Round 5 Chains 31, Residues 201, Estimated correctness of the model 48.1 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 4911 restraints for refining 2516 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3013 (Rfree = 0.000) for 2516 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 12: After refmac, R = 0.3007 (Rfree = 0.000) for 2469 atoms. Found 13 (22 requested) and removed 22 (11 requested) atoms. Cycle 13: After refmac, R = 0.2842 (Rfree = 0.000) for 2423 atoms. Found 16 (22 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2754 (Rfree = 0.000) for 2401 atoms. Found 14 (21 requested) and removed 16 (10 requested) atoms. Cycle 15: After refmac, R = 0.2608 (Rfree = 0.000) for 2382 atoms. Found 10 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2471 seeds are put forward Round 1: 223 peptides, 27 chains. Longest chain 18 peptides. Score 0.585 Round 2: 230 peptides, 22 chains. Longest chain 28 peptides. Score 0.662 Round 3: 228 peptides, 27 chains. Longest chain 18 peptides. Score 0.599 Round 4: 239 peptides, 25 chains. Longest chain 36 peptides. Score 0.650 Round 5: 247 peptides, 23 chains. Longest chain 29 peptides. Score 0.690 Taking the results from Round 5 Chains 28, Residues 224, Estimated correctness of the model 63.0 % 8 chains (103 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 4461 restraints for refining 2558 atoms. 3238 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3131 (Rfree = 0.000) for 2558 atoms. Found 17 (22 requested) and removed 52 (11 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2799 (Rfree = 0.000) for 2496 atoms. Found 10 (22 requested) and removed 25 (11 requested) atoms. Cycle 18: After refmac, R = 0.2942 (Rfree = 0.000) for 2455 atoms. Found 13 (22 requested) and removed 35 (11 requested) atoms. Cycle 19: After refmac, R = 0.2640 (Rfree = 0.000) for 2416 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. Cycle 20: After refmac, R = 0.2508 (Rfree = 0.000) for 2404 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 2474 seeds are put forward Round 1: 219 peptides, 24 chains. Longest chain 26 peptides. Score 0.611 Round 2: 233 peptides, 20 chains. Longest chain 24 peptides. Score 0.691 Round 3: 229 peptides, 21 chains. Longest chain 25 peptides. Score 0.671 Round 4: 243 peptides, 24 chains. Longest chain 25 peptides. Score 0.670 Round 5: 237 peptides, 26 chains. Longest chain 27 peptides. Score 0.634 Taking the results from Round 2 Chains 23, Residues 213, Estimated correctness of the model 63.2 % 5 chains (63 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 4642 restraints for refining 2464 atoms. 3614 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2850 (Rfree = 0.000) for 2464 atoms. Found 17 (22 requested) and removed 37 (11 requested) atoms. Cycle 22: After refmac, R = 0.2772 (Rfree = 0.000) for 2424 atoms. Found 18 (21 requested) and removed 19 (10 requested) atoms. Cycle 23: After refmac, R = 0.2450 (Rfree = 0.000) for 2417 atoms. Found 9 (21 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.2364 (Rfree = 0.000) for 2409 atoms. Found 1 (21 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.2354 (Rfree = 0.000) for 2396 atoms. Found 2 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 2457 seeds are put forward Round 1: 214 peptides, 25 chains. Longest chain 16 peptides. Score 0.586 Round 2: 215 peptides, 21 chains. Longest chain 19 peptides. Score 0.637 Round 3: 223 peptides, 28 chains. Longest chain 18 peptides. Score 0.573 Round 4: 240 peptides, 25 chains. Longest chain 23 peptides. Score 0.652 Round 5: 223 peptides, 25 chains. Longest chain 24 peptides. Score 0.610 Taking the results from Round 4 Chains 30, Residues 215, Estimated correctness of the model 54.3 % 7 chains (77 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 4704 restraints for refining 2591 atoms. 3588 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3018 (Rfree = 0.000) for 2591 atoms. Found 14 (23 requested) and removed 63 (11 requested) atoms. Cycle 27: After refmac, R = 0.2710 (Rfree = 0.000) for 2508 atoms. Found 11 (22 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.2700 (Rfree = 0.000) for 2488 atoms. Found 6 (22 requested) and removed 19 (11 requested) atoms. Cycle 29: After refmac, R = 0.2611 (Rfree = 0.000) for 2465 atoms. Found 14 (22 requested) and removed 17 (11 requested) atoms. Cycle 30: After refmac, R = 0.2610 (Rfree = 0.000) for 2456 atoms. Found 15 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 2526 seeds are put forward Round 1: 199 peptides, 26 chains. Longest chain 17 peptides. Score 0.529 Round 2: 224 peptides, 25 chains. Longest chain 18 peptides. Score 0.612 Round 3: 230 peptides, 29 chains. Longest chain 19 peptides. Score 0.579 Round 4: 222 peptides, 25 chains. Longest chain 20 peptides. Score 0.607 Round 5: 218 peptides, 27 chains. Longest chain 21 peptides. Score 0.571 Taking the results from Round 2 Chains 27, Residues 199, Estimated correctness of the model 44.3 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 5092 restraints for refining 2537 atoms. 4198 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2720 (Rfree = 0.000) for 2537 atoms. Found 15 (22 requested) and removed 30 (11 requested) atoms. Cycle 32: After refmac, R = 0.2929 (Rfree = 0.000) for 2507 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 33: After refmac, R = 0.2565 (Rfree = 0.000) for 2485 atoms. Found 17 (22 requested) and removed 19 (11 requested) atoms. Cycle 34: After refmac, R = 0.2372 (Rfree = 0.000) for 2466 atoms. Found 7 (22 requested) and removed 17 (11 requested) atoms. Cycle 35: After refmac, R = 0.2261 (Rfree = 0.000) for 2446 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 2527 seeds are put forward Round 1: 209 peptides, 27 chains. Longest chain 21 peptides. Score 0.545 Round 2: 214 peptides, 25 chains. Longest chain 21 peptides. Score 0.586 Round 3: 213 peptides, 26 chains. Longest chain 20 peptides. Score 0.570 Round 4: 226 peptides, 28 chains. Longest chain 19 peptides. Score 0.581 Round 5: 214 peptides, 21 chains. Longest chain 18 peptides. Score 0.635 Taking the results from Round 5 Chains 26, Residues 193, Estimated correctness of the model 50.2 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 5194 restraints for refining 2564 atoms. 4319 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3063 (Rfree = 0.000) for 2564 atoms. Found 23 (23 requested) and removed 58 (11 requested) atoms. Cycle 37: After refmac, R = 0.2848 (Rfree = 0.000) for 2497 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 38: After refmac, R = 0.2591 (Rfree = 0.000) for 2484 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 39: After refmac, R = 0.2453 (Rfree = 0.000) for 2480 atoms. Found 11 (22 requested) and removed 14 (11 requested) atoms. Cycle 40: After refmac, R = 0.2258 (Rfree = 0.000) for 2467 atoms. Found 9 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2544 seeds are put forward Round 1: 178 peptides, 23 chains. Longest chain 14 peptides. Score 0.506 Round 2: 212 peptides, 21 chains. Longest chain 20 peptides. Score 0.630 Round 3: 208 peptides, 22 chains. Longest chain 25 peptides. Score 0.607 Round 4: 213 peptides, 25 chains. Longest chain 29 peptides. Score 0.583 Round 5: 199 peptides, 22 chains. Longest chain 25 peptides. Score 0.583 Taking the results from Round 2 Chains 21, Residues 191, Estimated correctness of the model 48.9 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 8159 reflections ( 99.74 % complete ) and 4975 restraints for refining 2490 atoms. 4086 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2785 (Rfree = 0.000) for 2490 atoms. Found 15 (22 requested) and removed 22 (11 requested) atoms. Cycle 42: After refmac, R = 0.2643 (Rfree = 0.000) for 2476 atoms. Found 16 (22 requested) and removed 16 (11 requested) atoms. Cycle 43: After refmac, R = 0.2656 (Rfree = 0.000) for 2468 atoms. Found 19 (22 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.2593 (Rfree = 0.000) for 2467 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.2963 (Rfree = 0.000) for 2450 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.00 Search for helices and strands: 0 residues in 0 chains, 2537 seeds are put forward Round 1: 198 peptides, 27 chains. Longest chain 18 peptides. Score 0.512 Round 2: 214 peptides, 27 chains. Longest chain 20 peptides. Score 0.560 Round 3: 209 peptides, 23 chains. Longest chain 35 peptides. Score 0.597 Round 4: 219 peptides, 24 chains. Longest chain 18 peptides. Score 0.611 Round 5: 214 peptides, 23 chains. Longest chain 31 peptides. Score 0.611 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 191, Estimated correctness of the model 44.0 % 2 chains (31 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vmi-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (191 residues) following loop building 2 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8159 reflections ( 99.74 % complete ) and 5148 restraints for refining 2540 atoms. 4286 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3127 (Rfree = 0.000) for 2540 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.3216 (Rfree = 0.000) for 2503 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2951 (Rfree = 0.000) for 2475 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2816 (Rfree = 0.000) for 2457 atoms. TimeTaking 104.72