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 1vra-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.4-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/1vra-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.4-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/1vra-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.4-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 416 and 0 Target number of residues in the AU: 416 Target solvent content: 0.5943 Checking the provided sequence file Detected sequence length: 423 Maximum limit of NCS related copies: 30 Number of NCS-related molecules: 1 Adjusted target number of residues: 423 Adjusted target solvent content: 0.59 Input MTZ file: 1vra-3.4-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: 92 Cell parameters: 70.658 70.658 222.292 90.000 90.000 90.000 Input sequence file: 1vra-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3384 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.814 3.400 Wilson plot Bfac: 50.00 8346 reflections ( 99.71 % complete ) and 0 restraints for refining 3735 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3677 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3398 (Rfree = 0.000) for 3735 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 2.67 Search for helices and strands: 0 residues in 0 chains, 3794 seeds are put forward Round 1: 249 peptides, 41 chains. Longest chain 12 peptides. Score 0.436 Round 2: 276 peptides, 38 chains. Longest chain 21 peptides. Score 0.539 Round 3: 285 peptides, 36 chains. Longest chain 22 peptides. Score 0.581 Round 4: 294 peptides, 32 chains. Longest chain 28 peptides. Score 0.639 Round 5: 292 peptides, 27 chains. Longest chain 36 peptides. Score 0.680 Taking the results from Round 5 Chains 31, Residues 265, Estimated correctness of the model 52.6 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 6051 restraints for refining 3077 atoms. 4892 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3047 (Rfree = 0.000) for 3077 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 2: After refmac, R = 0.2897 (Rfree = 0.000) for 3028 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2772 (Rfree = 0.000) for 3020 atoms. Found 20 (22 requested) and removed 22 (11 requested) atoms. Cycle 4: After refmac, R = 0.2679 (Rfree = 0.000) for 2999 atoms. Found 14 (22 requested) and removed 18 (11 requested) atoms. Cycle 5: After refmac, R = 0.2627 (Rfree = 0.000) for 2984 atoms. Found 11 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 2.69 Search for helices and strands: 0 residues in 0 chains, 3091 seeds are put forward Round 1: 272 peptides, 38 chains. Longest chain 27 peptides. Score 0.530 Round 2: 299 peptides, 39 chains. Longest chain 28 peptides. Score 0.582 Round 3: 303 peptides, 33 chains. Longest chain 39 peptides. Score 0.648 Round 4: 306 peptides, 33 chains. Longest chain 26 peptides. Score 0.653 Round 5: 299 peptides, 30 chains. Longest chain 31 peptides. Score 0.667 Taking the results from Round 5 Chains 39, Residues 269, Estimated correctness of the model 49.0 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 5956 restraints for refining 3077 atoms. 4692 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3029 (Rfree = 0.000) for 3077 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 7: After refmac, R = 0.2772 (Rfree = 0.000) for 3054 atoms. Found 12 (23 requested) and removed 21 (11 requested) atoms. Cycle 8: After refmac, R = 0.2774 (Rfree = 0.000) for 3033 atoms. Found 15 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2712 (Rfree = 0.000) for 3026 atoms. Found 12 (22 requested) and removed 21 (11 requested) atoms. Cycle 10: After refmac, R = 0.2616 (Rfree = 0.000) for 3016 atoms. Found 2 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.70 Search for helices and strands: 0 residues in 0 chains, 3094 seeds are put forward Round 1: 259 peptides, 34 chains. Longest chain 26 peptides. Score 0.542 Round 2: 290 peptides, 30 chains. Longest chain 34 peptides. Score 0.649 Round 3: 298 peptides, 28 chains. Longest chain 43 peptides. Score 0.682 Round 4: 312 peptides, 32 chains. Longest chain 49 peptides. Score 0.673 Round 5: 284 peptides, 29 chains. Longest chain 29 peptides. Score 0.647 Taking the results from Round 3 Chains 30, Residues 270, Estimated correctness of the model 53.1 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 5681 restraints for refining 3077 atoms. 4360 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3007 (Rfree = 0.000) for 3077 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 12: After refmac, R = 0.2771 (Rfree = 0.000) for 3049 atoms. Found 12 (23 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.2646 (Rfree = 0.000) for 3042 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. Cycle 14: After refmac, R = 0.2576 (Rfree = 0.000) for 3032 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2538 (Rfree = 0.000) for 3026 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 2.69 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward Round 1: 273 peptides, 40 chains. Longest chain 22 peptides. Score 0.510 Round 2: 280 peptides, 33 chains. Longest chain 21 peptides. Score 0.600 Round 3: 273 peptides, 30 chains. Longest chain 24 peptides. Score 0.615 Round 4: 274 peptides, 34 chains. Longest chain 22 peptides. Score 0.577 Round 5: 275 peptides, 32 chains. Longest chain 21 peptides. Score 0.599 Taking the results from Round 3 Chains 35, Residues 243, Estimated correctness of the model 33.5 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 6083 restraints for refining 3077 atoms. 4981 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2846 (Rfree = 0.000) for 3077 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 17: After refmac, R = 0.2602 (Rfree = 0.000) for 3062 atoms. Found 5 (23 requested) and removed 19 (11 requested) atoms. Cycle 18: After refmac, R = 0.2565 (Rfree = 0.000) for 3040 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Cycle 19: After refmac, R = 0.2498 (Rfree = 0.000) for 3035 atoms. Found 8 (22 requested) and removed 19 (11 requested) atoms. Cycle 20: After refmac, R = 0.2482 (Rfree = 0.000) for 3021 atoms. Found 6 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.70 Search for helices and strands: 0 residues in 0 chains, 3111 seeds are put forward Round 1: 252 peptides, 36 chains. Longest chain 19 peptides. Score 0.502 Round 2: 285 peptides, 41 chains. Longest chain 19 peptides. Score 0.529 Round 3: 292 peptides, 34 chains. Longest chain 27 peptides. Score 0.616 Round 4: 269 peptides, 35 chains. Longest chain 21 peptides. Score 0.555 Round 5: 274 peptides, 34 chains. Longest chain 19 peptides. Score 0.577 Taking the results from Round 3 Chains 36, Residues 258, Estimated correctness of the model 33.8 % 5 chains (67 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 5938 restraints for refining 3077 atoms. 4710 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2950 (Rfree = 0.000) for 3077 atoms. Found 20 (23 requested) and removed 30 (11 requested) atoms. Cycle 22: After refmac, R = 0.2772 (Rfree = 0.000) for 3052 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. Cycle 23: After refmac, R = 0.2701 (Rfree = 0.000) for 3032 atoms. Found 8 (22 requested) and removed 14 (11 requested) atoms. Cycle 24: After refmac, R = 0.2651 (Rfree = 0.000) for 3023 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.2680 (Rfree = 0.000) for 3013 atoms. Found 8 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 2.69 Search for helices and strands: 0 residues in 0 chains, 3103 seeds are put forward Round 1: 272 peptides, 41 chains. Longest chain 20 peptides. Score 0.497 Round 2: 289 peptides, 37 chains. Longest chain 20 peptides. Score 0.580 Round 3: 291 peptides, 37 chains. Longest chain 25 peptides. Score 0.584 Round 4: 301 peptides, 35 chains. Longest chain 20 peptides. Score 0.625 Round 5: 295 peptides, 31 chains. Longest chain 20 peptides. Score 0.650 Taking the results from Round 5 Chains 33, Residues 264, Estimated correctness of the model 44.1 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 6328 restraints for refining 3077 atoms. 5216 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2958 (Rfree = 0.000) for 3077 atoms. Found 16 (23 requested) and removed 19 (11 requested) atoms. Cycle 27: After refmac, R = 0.2742 (Rfree = 0.000) for 3063 atoms. Found 11 (23 requested) and removed 18 (11 requested) atoms. Cycle 28: After refmac, R = 0.2619 (Rfree = 0.000) for 3050 atoms. Found 5 (23 requested) and removed 21 (11 requested) atoms. Cycle 29: After refmac, R = 0.2553 (Rfree = 0.000) for 3031 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.2507 (Rfree = 0.000) for 3021 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 2.73 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward Round 1: 253 peptides, 38 chains. Longest chain 18 peptides. Score 0.482 Round 2: 284 peptides, 32 chains. Longest chain 34 peptides. Score 0.618 Round 3: 271 peptides, 33 chains. Longest chain 22 peptides. Score 0.580 Round 4: 277 peptides, 30 chains. Longest chain 28 peptides. Score 0.623 Round 5: 286 peptides, 29 chains. Longest chain 30 peptides. Score 0.651 Taking the results from Round 5 Chains 34, Residues 257, Estimated correctness of the model 44.4 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 6023 restraints for refining 3077 atoms. 4855 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2849 (Rfree = 0.000) for 3077 atoms. Found 16 (23 requested) and removed 23 (11 requested) atoms. Cycle 32: After refmac, R = 0.2626 (Rfree = 0.000) for 3058 atoms. Failed to save intermediate PDB Found 14 (23 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2557 (Rfree = 0.000) for 3053 atoms. Found 8 (23 requested) and removed 15 (11 requested) atoms. Cycle 34: After refmac, R = 0.2541 (Rfree = 0.000) for 3043 atoms. Found 5 (22 requested) and removed 15 (11 requested) atoms. Cycle 35: After refmac, R = 0.2516 (Rfree = 0.000) for 3030 atoms. Found 10 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 2.69 Search for helices and strands: 0 residues in 0 chains, 3115 seeds are put forward Round 1: 241 peptides, 37 chains. Longest chain 19 peptides. Score 0.461 Round 2: 264 peptides, 34 chains. Longest chain 20 peptides. Score 0.554 Round 3: 270 peptides, 31 chains. Longest chain 24 peptides. Score 0.598 Round 4: 263 peptides, 32 chains. Longest chain 22 peptides. Score 0.572 Round 5: 265 peptides, 34 chains. Longest chain 23 peptides. Score 0.556 Taking the results from Round 3 Chains 32, Residues 239, Estimated correctness of the model 28.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 6406 restraints for refining 3077 atoms. 5358 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2768 (Rfree = 0.000) for 3077 atoms. Found 19 (23 requested) and removed 24 (11 requested) atoms. Cycle 37: After refmac, R = 0.2605 (Rfree = 0.000) for 3067 atoms. Found 4 (23 requested) and removed 15 (11 requested) atoms. Cycle 38: After refmac, R = 0.2536 (Rfree = 0.000) for 3052 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.2480 (Rfree = 0.000) for 3039 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.2469 (Rfree = 0.000) for 3030 atoms. Found 5 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.69 Search for helices and strands: 0 residues in 0 chains, 3081 seeds are put forward Round 1: 227 peptides, 33 chains. Longest chain 20 peptides. Score 0.471 Round 2: 268 peptides, 32 chains. Longest chain 23 peptides. Score 0.584 Round 3: 258 peptides, 31 chains. Longest chain 22 peptides. Score 0.571 Round 4: 244 peptides, 29 chains. Longest chain 18 peptides. Score 0.560 Round 5: 253 peptides, 32 chains. Longest chain 21 peptides. Score 0.549 Taking the results from Round 2 Chains 34, Residues 236, Estimated correctness of the model 23.4 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8346 reflections ( 99.71 % complete ) and 6408 restraints for refining 3077 atoms. 5430 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2560 (Rfree = 0.000) for 3077 atoms. Found 9 (23 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.2466 (Rfree = 0.000) for 3067 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. Cycle 43: After refmac, R = 0.2460 (Rfree = 0.000) for 3054 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.2462 (Rfree = 0.000) for 3041 atoms. Found 6 (22 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.2430 (Rfree = 0.000) for 3033 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 2.68 Search for helices and strands: 0 residues in 0 chains, 3112 seeds are put forward Round 1: 235 peptides, 35 chains. Longest chain 20 peptides. Score 0.469 Round 2: 264 peptides, 38 chains. Longest chain 20 peptides. Score 0.510 Round 3: 252 peptides, 35 chains. Longest chain 22 peptides. Score 0.513 Round 4: 247 peptides, 30 chains. Longest chain 32 peptides. Score 0.556 Round 5: 255 peptides, 33 chains. Longest chain 25 peptides. Score 0.543 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 217, Estimated correctness of the model 13.7 % 5 chains (60 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 1vra-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (217 residues) following loop building 5 chains (60 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8346 reflections ( 99.71 % complete ) and 6106 restraints for refining 3077 atoms. 5082 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2779 (Rfree = 0.000) for 3077 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2658 (Rfree = 0.000) for 3059 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2607 (Rfree = 0.000) for 3048 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 49: After refmac, R = 0.2564 (Rfree = 0.000) for 3035 atoms. TimeTaking 55.2