null Sun 23 Dec 22:22:46 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vra-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vra-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-4.0-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 22:22:56 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-4.0-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 377 and 0 Target number of residues in the AU: 377 Target solvent content: 0.6323 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3384 target number of atoms Had to go as low as 0.85 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 4.000 Wilson plot Bfac: 67.61 5212 reflections ( 99.54 % complete ) and 0 restraints for refining 3728 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3796 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3783 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.13 Search for helices and strands: 0 residues in 0 chains, 3806 seeds are put forward Round 1: 178 peptides, 34 chains. Longest chain 8 peptides. Score 0.314 Round 2: 214 peptides, 32 chains. Longest chain 17 peptides. Score 0.448 Round 3: 250 peptides, 31 chains. Longest chain 21 peptides. Score 0.553 Round 4: 257 peptides, 34 chains. Longest chain 26 peptides. Score 0.537 Round 5: 248 peptides, 31 chains. Longest chain 27 peptides. Score 0.548 Taking the results from Round 3 Chains 31, Residues 219, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6828 restraints for refining 3055 atoms. 5940 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3282 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 43 (7 requested) atoms. Cycle 2: After refmac, R = 0.2949 (Rfree = 0.000) for 2968 atoms. Found 14 (14 requested) and removed 32 (7 requested) atoms. Cycle 3: After refmac, R = 0.2808 (Rfree = 0.000) for 2914 atoms. Found 14 (14 requested) and removed 41 (7 requested) atoms. Cycle 4: After refmac, R = 0.2657 (Rfree = 0.000) for 2864 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 5: After refmac, R = 0.2574 (Rfree = 0.000) for 2836 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.10 Search for helices and strands: 0 residues in 0 chains, 2935 seeds are put forward Round 1: 229 peptides, 37 chains. Longest chain 19 peptides. Score 0.428 Round 2: 241 peptides, 29 chains. Longest chain 26 peptides. Score 0.553 Round 3: 242 peptides, 29 chains. Longest chain 17 peptides. Score 0.555 Round 4: 242 peptides, 28 chains. Longest chain 23 peptides. Score 0.566 Round 5: 250 peptides, 28 chains. Longest chain 26 peptides. Score 0.585 Taking the results from Round 5 Chains 31, Residues 222, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6473 restraints for refining 3056 atoms. 5511 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3040 (Rfree = 0.000) for 3056 atoms. Found 14 (14 requested) and removed 42 (7 requested) atoms. Cycle 7: After refmac, R = 0.2778 (Rfree = 0.000) for 2977 atoms. Found 14 (14 requested) and removed 41 (7 requested) atoms. Cycle 8: After refmac, R = 0.2648 (Rfree = 0.000) for 2933 atoms. Found 11 (14 requested) and removed 25 (7 requested) atoms. Cycle 9: After refmac, R = 0.2559 (Rfree = 0.000) for 2899 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.2193 (Rfree = 0.000) for 2878 atoms. Found 5 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.16 Search for helices and strands: 0 residues in 0 chains, 2968 seeds are put forward Round 1: 228 peptides, 37 chains. Longest chain 17 peptides. Score 0.425 Round 2: 245 peptides, 32 chains. Longest chain 21 peptides. Score 0.529 Round 3: 262 peptides, 32 chains. Longest chain 22 peptides. Score 0.570 Round 4: 252 peptides, 30 chains. Longest chain 20 peptides. Score 0.568 Round 5: 257 peptides, 32 chains. Longest chain 21 peptides. Score 0.558 Taking the results from Round 3 Chains 35, Residues 230, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6351 restraints for refining 3055 atoms. 5310 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3017 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 40 (7 requested) atoms. Cycle 12: After refmac, R = 0.2736 (Rfree = 0.000) for 2974 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 13: After refmac, R = 0.2704 (Rfree = 0.000) for 2938 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 14: After refmac, R = 0.2602 (Rfree = 0.000) for 2912 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 15: After refmac, R = 0.2582 (Rfree = 0.000) for 2893 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.10 Search for helices and strands: 0 residues in 0 chains, 3005 seeds are put forward Round 1: 220 peptides, 33 chains. Longest chain 16 peptides. Score 0.452 Round 2: 236 peptides, 31 chains. Longest chain 21 peptides. Score 0.518 Round 3: 227 peptides, 33 chains. Longest chain 16 peptides. Score 0.471 Round 4: 225 peptides, 31 chains. Longest chain 17 peptides. Score 0.490 Round 5: 245 peptides, 27 chains. Longest chain 21 peptides. Score 0.584 Taking the results from Round 5 Chains 28, Residues 218, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6633 restraints for refining 3055 atoms. 5688 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2943 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 68 (7 requested) atoms. Cycle 17: After refmac, R = 0.2670 (Rfree = 0.000) for 2969 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 18: After refmac, R = 0.2638 (Rfree = 0.000) for 2935 atoms. Found 14 (14 requested) and removed 35 (7 requested) atoms. Cycle 19: After refmac, R = 0.2605 (Rfree = 0.000) for 2905 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 20: After refmac, R = 0.2637 (Rfree = 0.000) for 2882 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.08 Search for helices and strands: 0 residues in 0 chains, 2984 seeds are put forward Round 1: 225 peptides, 42 chains. Longest chain 13 peptides. Score 0.354 Round 2: 225 peptides, 36 chains. Longest chain 15 peptides. Score 0.429 Round 3: 228 peptides, 35 chains. Longest chain 19 peptides. Score 0.450 Round 4: 213 peptides, 30 chains. Longest chain 20 peptides. Score 0.470 Round 5: 216 peptides, 33 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 4 Chains 31, Residues 183, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6837 restraints for refining 3055 atoms. 6045 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2826 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 22: After refmac, R = 0.2654 (Rfree = 0.000) for 3010 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 23: After refmac, R = 0.2505 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 24: After refmac, R = 0.2563 (Rfree = 0.000) for 2943 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 25: After refmac, R = 0.2618 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.03 Search for helices and strands: 0 residues in 0 chains, 3075 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 8 peptides. Score 0.285 Round 2: 219 peptides, 35 chains. Longest chain 26 peptides. Score 0.425 Round 3: 221 peptides, 35 chains. Longest chain 16 peptides. Score 0.430 Round 4: 223 peptides, 38 chains. Longest chain 13 peptides. Score 0.399 Round 5: 225 peptides, 38 chains. Longest chain 17 peptides. Score 0.404 Taking the results from Round 3 Chains 36, Residues 186, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6699 restraints for refining 3056 atoms. 5892 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2612 (Rfree = 0.000) for 3056 atoms. Found 14 (14 requested) and removed 39 (7 requested) atoms. Cycle 27: After refmac, R = 0.2472 (Rfree = 0.000) for 3005 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 28: After refmac, R = 0.2446 (Rfree = 0.000) for 2977 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 29: After refmac, R = 0.2292 (Rfree = 0.000) for 2955 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 30: After refmac, R = 0.2321 (Rfree = 0.000) for 2939 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.09 Search for helices and strands: 0 residues in 0 chains, 3063 seeds are put forward Round 1: 189 peptides, 36 chains. Longest chain 12 peptides. Score 0.321 Round 2: 221 peptides, 36 chains. Longest chain 12 peptides. Score 0.418 Round 3: 226 peptides, 37 chains. Longest chain 13 peptides. Score 0.420 Round 4: 229 peptides, 35 chains. Longest chain 18 peptides. Score 0.453 Round 5: 226 peptides, 35 chains. Longest chain 22 peptides. Score 0.444 Taking the results from Round 4 Chains 38, Residues 194, Estimated correctness of the model 0.0 % 7 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6514 restraints for refining 3056 atoms. 5621 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2706 (Rfree = 0.000) for 3056 atoms. Found 14 (14 requested) and removed 38 (7 requested) atoms. Cycle 32: After refmac, R = 0.2420 (Rfree = 0.000) for 2999 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 33: After refmac, R = 0.2341 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 34: After refmac, R = 0.2260 (Rfree = 0.000) for 2958 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 35: After refmac, R = 0.2211 (Rfree = 0.000) for 2946 atoms. Found 10 (14 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.05 Search for helices and strands: 0 residues in 0 chains, 3049 seeds are put forward Round 1: 200 peptides, 36 chains. Longest chain 15 peptides. Score 0.356 Round 2: 215 peptides, 35 chains. Longest chain 14 peptides. Score 0.413 Round 3: 220 peptides, 33 chains. Longest chain 15 peptides. Score 0.452 Round 4: 208 peptides, 30 chains. Longest chain 21 peptides. Score 0.456 Round 5: 214 peptides, 33 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 4 Chains 32, Residues 178, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 6817 restraints for refining 3056 atoms. 6070 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2663 (Rfree = 0.000) for 3056 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 37: After refmac, R = 0.2363 (Rfree = 0.000) for 3025 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 38: After refmac, R = 0.2519 (Rfree = 0.000) for 3004 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 39: After refmac, R = 0.2321 (Rfree = 0.000) for 2980 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 40: After refmac, R = 0.2306 (Rfree = 0.000) for 2959 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.10 Search for helices and strands: 0 residues in 0 chains, 3085 seeds are put forward Round 1: 174 peptides, 34 chains. Longest chain 11 peptides. Score 0.301 Round 2: 199 peptides, 33 chains. Longest chain 11 peptides. Score 0.392 Round 3: 190 peptides, 30 chains. Longest chain 12 peptides. Score 0.405 Round 4: 198 peptides, 30 chains. Longest chain 13 peptides. Score 0.428 Round 5: 196 peptides, 28 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 5 Chains 28, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5212 reflections ( 99.54 % complete ) and 7099 restraints for refining 3055 atoms. 6455 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2834 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 42: After refmac, R = 0.2548 (Rfree = 0.000) for 3015 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 43: After refmac, R = 0.2472 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 44: After refmac, R = 0.2409 (Rfree = 0.000) for 2950 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 45: After refmac, R = 0.2668 (Rfree = 0.000) for 2934 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.10 Search for helices and strands: 0 residues in 0 chains, 3056 seeds are put forward Round 1: 162 peptides, 33 chains. Longest chain 10 peptides. Score 0.275 Round 2: 198 peptides, 35 chains. Longest chain 12 peptides. Score 0.363 Round 3: 204 peptides, 31 chains. Longest chain 14 peptides. Score 0.432 Round 4: 204 peptides, 32 chains. Longest chain 15 peptides. Score 0.420 Round 5: 196 peptides, 27 chains. Longest chain 13 peptides. Score 0.460 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 169, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vra-4_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (169 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5212 reflections ( 99.54 % complete ) and 6834 restraints for refining 3056 atoms. 6164 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2611 (Rfree = 0.000) for 3056 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2496 (Rfree = 0.000) for 3029 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2572 (Rfree = 0.000) for 3011 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2651 (Rfree = 0.000) for 2992 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:53 GMT 2018 Job finished. TimeTaking 55.11 Used memory is bytes: 20154968